Publications
A correlated frailty model is suggested for analysis of bivariate time-to-event data. The model is an extension of the correlated power variance function (PVF) frailty model (correlated three-...
Objectives: The aim of this study was to evaluate the use of high resolution CT to radiologically define teeth filling material properties in terms of Hounsfield units after high temperature...
Background Previous studies have suggested that breast cancer risk factors are associated with estrogen receptor (ER) and progesterone receptor (PR) expression status of the tumors. Methods We...
In [A.-K. Tornberg, B. Engquist, Numerical approximations of singular source terms in differential equations, J. Comput. Phys. 200 (2004) 462-488], it was shown for simple examples that the then...
The generation of internal waves from barotropic tides can be quantified in terms of the conversion rates. These have often been obtained by applying the WKB approximation, which yields an...
The schematic visualization of the Alq(3) molecule on the Fe substrate with the optimized geometry at lowest total energy. When the Alq(3) molecule is relaxed on the surface, only two of the wings...
This paper reports the working mechanism for a redox-responsive bistable [2]rotaxane incorporating an alpha-cyclodextrin (alpha-CD) ring (J. Am. Chem. Soc. 2008, 130, 11294-11296), based on free...
Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose I beta. The latest version of the GLYCAM force field series (...
Motivation: The precise prediction of one-dimensional (1D) protein structure as represented by the protein secondary structure and 1D string of discrete state of dihedral angles (i.e. Shape...
In several biologically relevant situations, cell locomotion occurs in polymeric fluids with Weissenberg number larger than 1. Here we present results of three-dimensional numerical simulations...
The interaction between para-crystalline cellulose and the cross-linking glycan xyloglucan (XG) plays a central role for the strength and extensibility of plant cell walls. The coating of XGs on...
We examine the experimental absence of standing spin wave modes in thin magnetic films, by means of atomistic spin dynamics simulations. Using Co on Cu(001) as a model system, we demonstrate that...
The origin of the anomalous, 400% increase of the piezoelectric coefficient in Sc(x)Al(1-x)N alloys is revealed. Quantum mechanical calculations show that the effect is intrinsic. It comes from a...
Strong compositional-dependent elastic properties have been observed theoretically and experimentally in Ti(1-x)Al(x)N alloys. The elastic constant, C(11), changes by more than 50% depending on...
Two binder candidates 4-C37L34-B and 3-C15L8-B from a 16-membered set of 42-residue polypeptide conjugates designed to bind human carbonic anhydrase II (HCAII), were shown to bind HCAII with high...
A parabolised set of equations is used to compute spatial optimal disturbances in Falkner-Skan-Cooke boundary layers These disturbances associated with maximum energy growth initially take the...
A parabolized set of linear equations is derived, which, in combination with the proposed solution procedure, allows for the study of both non-modal and modal disturbance growth in three-...
A systematic molecular dynamics (MD) study of zinc binding to a peptide that mimics the structural binding site of horse liver alcohol dehydrogenase (HLADH) has been conducted. The four zinc...
The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model...
7C8 is a mouse monoclonal antibody specific for the third hypervariable region (V3) of the human immunodeficiency virus type 2 (HIV-2)-associated protein gp125. The three-dimensional crystal...
Self-assembled monolayers and multilayers of a noradrenaline analogue (Nor-Pt) on gold substrates as well as multilayers of noradrenaline have been investigated by means of the molecular...
High-resolution simulations of forced quasi-geostrophic (QG) turbulence reveal that Charney isotropy develops under a wide range of conditions, and constitutes a preferred state also in beta-plane...
Molecular dynamics (MD) simulations form a powerful tool that is complementary to experiments and theory. They allow detailed investigations of both biological and chemical systems at the atomic...
Human monoclonal antibodies (mAbs) can routinely be isolated from phage display libraries against virtually any protein available in sufficient purity and quantity, but library design can...
Methods to parametrize coarse-grained simulation models for molecular fluids frequently either attempt to match the fluid structure (e g, pair correlation functions) previously obtained with...
The relativistic four-component static exchange approach for calculation of near-edge X-ray absorption spectra has been reviewed. Application of the method is made to the Au(111) interface and the...
The near carbon K-edge X-ray absorption and circular dichroism spectra of noradrenaline (neutral and protonated forms) and L-DOPA (protonated form) have been determined with use of the complex...
An algorithm for the solution of the linear response equation in the random phase approximation is presented. All entities including frequency arguments, matrices, and vectors, are assumed to be...
Secondary organic aerosol (SOA) particles are formed in the atmosphere from condensable oxidation products of anthropogenic and biogenic volatile organic compounds (VOCs)(1-7). On a global scale,...
The Monte Carlo method based on two-dimensional entropic sampling within the WangLandau (WL) algorithm is applied to simulation of a continuous model of a polyelectrolyte between membrane surfaces...
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-...
The use of a two-dimensional statistical passive vortex generator model, applied to an adverse pressure gradient boundary-layer flow, is evaluated qualitatively against experimental and fully...
The spatial and temporal development of a spray strongly depends on the local characteristics of turbulence. The turbulence-droplet coupling gives rise to droplet dispersion, which is the...
This paper provides a continuing study to the recent study by the authors and the results presented herein are based on the same numerical experiments enriching the previously obtained picture (...
The paper is mainly focused to the vast number of researchers who work within direct injection (DI) engine fuel spray simulations. The most common simulation framework today within the community...
Classical simulations of simple water models reproduce many properties of the liquid and ice but overestimate the heat capacity by about 65% at ordinary temperatures and much more for low...
Background: Working memory (WM) is the ability to retain task relevant information. This ability is important for a wide range of cognitive tasks, and WM deficits are a central cognitive...
This article presents a novel nonreflective boundary condition for the free surface incompressible Euler and Navier-Stokes equations. Boundaries of this type are very useful when, for example,...
Proinflammatory cytokines have been used for several years in patients with advanced cancer but their administration is typically associated with severe toxicity hampering their application to...
Chemical liabilities, such as adverse effects and toxicity, have a major impact on today's drug discovery process. In silk prediction of chemical liabilities is an important approach which can...
A: The HIV Drug Research Centre (HIVDRC) has established Web services for prediction of drug susceptibility for HIV proteases and reverse transcriptases. The services are based on two...
We synthesised observations of total particle number (CN) concentration from 36 sites around the world. We found that annual mean CN concentrations are typically 300-2000 cm(-3) in the marine...
This tutorial review describes an atomistic simulation approach to studies of dynamics of charge transport in pi-conjugated molecular or polymer based materials. The approach, which is termed...
Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] has been generalized to the propagation of the electronic wave functions. The...
We carried out a combined experimental and theoretical study of grain boundaries in polycrystalline diamond, aimed at achieving the conditions in which grain boundaries are equilibrated. Raman...
A fully coupled atmosphere-ocean general circulation model is used to simulate climate conditions during the last glacial maximum (LGM). Forcing conditions include astronomical parameters,...
Motivation: New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the 'novel'...
OBJECTIVE-Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired beta-cell function, raised glucose levels, insulin resistance...
An Eulerian turbulent two phase flow model using kinetic theory of granular flows for the particle phase was developed in order to study evolving upward turbulent gas particle flows in a pipe. The...
The correlation correlation between the fluctuating particle and gas velocity in isotropic turbulence is studied with a set of stochastic differential equations taking into account both particle-...
Chain packing in homogeneous blends of carbonate (13)C-labeled bisphenol A polycarbonate with either (i) CF(3)-labeled bisphenol A polycarbonate or (ii) ring-F-labeled bisphenol A polycarbonate...
Background: Chronic fatigue syndrome is an idiopathic syndrome widely suspected of having an infectious or immune etiology. We applied an unbiased metagenomic approach to try to identify known or...
In this paper we investigate a heterogeneous multiscale method (HMM) for interface tracking and apply the technique to the simulation of epitaxial growth. HMM relies on an efficient coupling...
We highlight Resonant Raman scattering as a dynamical process with a finite duration time that results from not only the irreversible homogeneous broadening but also the reversible dephasing...
We investigated the resonant x-ray emission from a neon atom induced by the two-photon population of a double-core-hole excited state. Two qualitatively different schemes of this process are...
Scattering process between a negative polaron and an exciton in a polymer chain is investigated by using the Su-Schrieffer-Heeger model modified to include electron-electron interactions, the...
By using the Su-Schrieffer-Heeger model modified to include electron-electron interactions, the Brazovskii-Kirova symmetry breaking term and an external electric field, we investigate the...
In recent years, many volumetric illumination models have been proposed, which have the potential to simulate advanced lighting effects and thus support improved image comprehension. Although...
Background: The link between squamous cell cervical carcinoma and human papillomavirus (HPV) 16/18 is well established, but the magnitude of the risk association is uncertain and the importance of...
Mutations in dynamin-2 (DNM2) cause autosomal dominant centronuclear myopathy (CNM). We report a series of 12 patients from eight families with CNM in whom we have identified a number of novel...
Energy fluxes important for determining the Arctic surface temperatures during winter in present-day simulations from the Coupled Model lntercomparison Project phase 3 (CMIP3) multimodel dataset...
Virtual screening of a library of commercially available compounds versus the structure of Mycobacterium tuberculosis lumazine synthase identified 2-(2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamido...
There is a great need for standards in the orthology field. Users must contend with different ortholog data representations from each provider, and the providers themselves must independently...
Receptivity, disturbance growth and transition to turbulence of the three-dimensional boundary layer developing on a swept flat plate are studied by means of numerical simulations. The flow is...
We show the response of the boundary-layer flow past a wing to free-stream disturbances with axial, vertical and spanwise vorticity and explain the associated receptivity mechanisms. A flat plate...
Receptivity of the two-dimensional boundary layer on a flat plate with elliptic leading edge is studied by numerical simulation. Vortical perturbations in the oncoming free stream are considered,...
Receptivity, disturbance growth and breakdown to turbulence in Gortler flow are studied by spatial direct numerical simulation (DNS). The boundary layer is exposed to free-stream vortical modes...
Background: The antibody-based targeted delivery of bioactive molecules to tumour vasculature is an attractive avenue to concentrate therapeutic agents at cancer sites, while sparing normal organs...
The activation of voltage-gated ion channels is controlled by the S4 helix, with arginines every third residue. The x-ray structures are believed to reflect an open-inactivated state, and models...
Grid computing has been the subject of many large national and international IT projects. However, not all goals of these projects have been achieved. In particular. the number of users lags...
The insulin-like growth factor 1 receptor (IGF-1R) plays crucial roles in developmental and cancer biology. Most of its biological effects have been ascribed to its tyrosine kinase activity, which...
Using a number of localized sensors and actuators, a feedback controller is designed in order to reduce the growth of three-dimensional disturbances in the hotplate boundary layer. A reduced-order...
The attenuation of three-dimensional wavepackets of streaks and Tollmien-Schlichting (TS) waves in a transitional boundary layer using feedback control is investigated numerically. Arrays of...
A series of asymmetrically substituted free-base di- and tetra-phenylporphyrins and the associated Zn-phenylporphyrins were synthesized and studied by X-ray diffraction, NMR, infrared, electronic...
This report covers various issues related to heat and mass transport in carbon nanotubes. Heat and mass transport under quasi-one-dimensional confinement has been investigated using molecular...
Kalign2 is one of the fastest and most accurate methods for multiple alignments. However, in contrast to other methods Kalign2 does not allow externally supplied position specific gap penalties....
A method to acquire multiple displacement encoded slices within a single breath hold is presented. Efficiency is improved over conventional DENSE without compromising image quality by readout of...
Aim: The influences on the signal-to-noise ratio (SNR) of Displacement ENcoding with Stimulated Echoes (DENSE) MRI of field strength, receiver coil sensitivity and choice of flip angle strategy...
This study proposes a computational model for attentional blink or "blink of the mind," a phenomenon where a human subject misses perception of a later expected visual pattern as two expected...
The early B-cell factor (EBF) transcription factors are central regulators of development in several organs and tissues. This protein family shows low sequence similarity to other protein families...
Platinum(II) and phosphine MM3 force field parameters are derived from fits to the ground state potential energy surface at the level of Kohn-Sham density functional theory with employment of the...
CHARMM force field parameter values for a class of oligothiophene derivatives have been derived with reference to density functional theory/B3LYP potential energy surfaces. The force field...
Purpose - A precise and rapid temperature cycling of a small volume of fluid is vital for an effective DNA replication process using the polymerase chain reaction (PCR). The purpose of this paper...
Non-Hodgkin lymphoma (NHL) represents a diverse group of hematological malignancies, of which follicular lymphoma (FL) is a prevalent subtype. A previous genome-wide association study has...
Ultraviolet radiation (UVR) exposure may influence risk of non-Hodgkin lymphoma (NHL) through vitamin D, with antineoplastic effects mediated through the vitamin D receptor (VDR). To explore the...
A jet in crossflow with an inflow ratio of 3, based on the maximum velocity of the parabolic jet profile, is studied numerically. The jet is modeled as an inhomogeneous boundary condition at the...
Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical...
Motivation: Learning-based model quality assessment programs have been quite successful at discriminating between high-and low-quality protein structures. Here, we show that it is possible to...
Turbulent spots ale studied in a boundary layer subject to freestream turbulence with the data taken from direct numerical simulations performed by Brandt et al. [2] Additional simulations of...
Vascular endothelial growth factor C (VEGF-C) is a key mediator of lymphangiogenesis, acting via its receptors VEGF-R2 and VEGF-R3. High expression of VEGF-C in tumors correlates with increased...
A spin-flip time dependent density functional theory approach with hybrid non-collinear exchange-correlation kernels has been applied to investigate the energy gap between the lowest singlet and...
We show that ultrasmall metallic nanoparticles can be combined with large second- and third-order response organic chromophores to enhance the overall third-order response of the system. This...
A general density functional theory/molecular mechanics approach for computation of electronic g-tensors of solvated molecules is presented. We apply the theory to the commonly studied di-tert-...
A density functional restricted unrestricted approach, capable of evaluating hyperfine coupling constants with the inclusion of spin polarization effects in a spin-restricted Kohn-Sham method, has...
We analyze the ability of spin-flip time dependent density functional theory (TD-DFT) to uniformly describe excited states of single, double, and mixed excitation character in closed-shell...
Purpose: Eddy current induced velocity offsets are of concern for accuracy in cardiovascular magnetic resonance (CMR) volume flow quantification. However, currently known theoretical aspects of...
This paper addresses recent developments in model-reduction techniques applicable to fluid flows The main goal is to obtain low-order models tractable enough to be used for analysis and design of...
The anion transporter I (ANTRI) from Arabidopsis thaliana, homologous to the mammalian members of the solute carrier 17 (SLC17) family, is located in the chloroplast thylakoid membrane. When...
Service-oriented computing is becoming an increasingly popular paradigm for modelling and building distributed systems in open and heterogeneous environments. However, proposed service-oriented...
This paper describes the third full release of the Rossby Centre Regional Climate model (RCA3), with an emphasis on changes compared to earlier versions, in particular the introduction of a new...
Molecular dynamics (MD) simulations of glycylglycine dipeptide with transition metal ions (Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+)) in aqueous solutions have been carried out to get an...
Acoustical and molecular dynamics studies were carried out to understand the various interactions present in glycylglycine-CuCl(2) aqueous solutions. Amongst these interactions, hydrogen bonding...
The temperature dependence of the heat conductivity has been obtained for a liquid crystal model based on the Gay-Berne fluid, from the isotropic phase at high temperatures through the nematic...
We have reviewed the work on molecular dynamics simulation of transport properties of liquid crystals during the last 25 years. To begin with, we present the model systems that have been used in...
We have applied a nonequilibrium molecular dynamics heat flow algorithm to calculate the heat conductivity of a molecular model system, which forms uniaxial and biaxial nematic liquid crystals....
This review summarizes recent first-principles investigations of the electronic structure and magnetism of dilute magnetic semiconductors (DMSs), which are interesting for applications in...
The evolution of disturbances in boundary layers modified through span-wise periodic, steady streamwise streaks is studied via numerical simulations The disturbances are introduced via random two...
A well-resolved large-eddy simulation (LES) of a spatially developing turbulent boundary layer under zero-pressure-gradient up to comparably high Reynolds numbers (Re(theta) = 4300) is performed....
Turbulent flow close to solid walls is dominated by an ensemble of fluctuations of large and small spatial scales. Recent work by Mathis [J. Fluid Mech. 628, 311 (2009); Phys. Fluids 21, 111703 (...
Photoswitching molecules are attractive candidates as organic materials for optoelectronics applications because light impulses can switch them between states with different conducting...
Geometric integration schemes for extended Lagrangian self-consistent Born-Oppenheimer molecular dynamics, including a weak dissipation to remove numerical noise, are developed and analyzed. The...
The influence of the electrode's Fermi surface on the transport properties of a photoswitching molecule is investigated with state-of-the-art ab initio transport methods. We report results for the...
A direct numerical simulation (DNS) of turbulent flow in a three-dimensional diffuser at Re = 10 000 (based on bulk velocity and inflow-duct height) was performed with a massively parallel high-...
The two-photon absorption (TPA) properties of four TPEB [tetrakis(phenylethynyl)benzene] derivatives (TD, para, ortho, and meta) with different donor/acceptor substitution patterns have been...
We present a brief overview of recent theoretical studies of the core-level binding energy shift (CLS) in solid metallic materials. The focus is on first principles calculations using the complete...
We use first-principles calculations of layer-resolved core-level binding energy shifts (CLSs) within density functional theory as away to characterize the interface quality and thickness in...
Context: The previously reported absence of 65-kDa glutamate decarboxylase antibody (GAD65Ab)-specific antiidiotypic antibodies (anti-Id) in type 1 diabetes (T1D) patients at clinical onset could...
Genes involved in cancer susceptibility and progression can serve as templates for searching protein networks for novel cancer genes. To this end, we introduce a general network searching method,...
The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the...
The total downwelling shortwave (SWID) and longwave (LWD) radiation and its components are assessed for the limited-area version of the Global Environmental Multiscale Model (GEM-LAM) against...
We generated and characterized novel antibody-cytokine fusion proteins ("immunocytokines") based on murine interleukin-7 (IL7), an immunomodulatory protein which has previously shown anti-cancer...
This paper presents gradienTv, a distributed, market-based approach to live streaming. In gradienTv, multiple streaming trees are constructed using a market-based approach, such that nodes with...
A wind tunnel experiment on laminar-turbulent transition has been performed in ETW (the European Transonic Wind Tunnel in Koln) at high Reynolds number and cryogenic conditions. The studied...
The importance of autopsy procedures leading to the establishment of the cause of death is well-known. A recent addition to the autopsy work flow is the possibility of conducting postmortem...
Background/Aims: Sepsis-induced lung injury is characterized by pulmonary hypertension, edema and deteriorated gas exchange. As in vivo studies have indicated that bacterial endotoxin...
Internal splittings in the spectra are due to quantized angular momentum field of the molecule or atom, which couples through spin-spin and spin-orbit operators. These operators are subjected to...
Phase contrast MRI is a powerful tool for the assessment of blood flow. However, especially in the highly complex and turbulent flow that accompanies many cardiovascular diseases, phase contrast...
The mechanisms for explaining how a stable asymmetric chemical system can be formed from a symmetric chemical system, in the absence of any asymmetric influence other than statistical fluctuations...
We propose and analyze a fast method for computing the solution of the high frequency Helmholtz equation in a bounded one-dimensional domain with a variable wave speed function. The method is...
In the present investigation, Direct Numerical Simulation (DNS) is used to study a binary irreversible and isothermal reaction in a plane turbulent wall-jet. The flow is compressible and a single-...
The two-dimensional flow around a rotating circular cylinder is studied at Re = 100. The instability mechanisms for the first and second shedding modes are analysed. The region in the flow with a...
The contribution of submarine groundwater discharge (SGD) to the total hydrological discharges to the sea may be large but has been difficult to quantify. We have tested the applicability and...
In mean-field magnetohydrodynamics the mean electromotive force due to velocity and magnetic-field fluctuations plays a crucial role. In general it consists of two parts, one independent of and...
Certain aspects of the mean-field theory of turbulent passive scalar transport and of mean-field electrodynamics are considered with particular emphasis on aspects of compressible fluids. It is...
We have performed Car-Parrinello mixed quantum mechanics/molecular mechanics (CP-QM/MM) calculations for stilbazolium merocyanine (SM) in polar and nonpolar solvents in order to explore the role...
We have studied the structures and absorption spectra of merocyanine, the photoresponsive isomer of the spiropyran (SP) merocyanine (MC) pair, in chloroform and in water solvents using a combined...
Based on hybrid QM/MM simulation techniques, we rationalize the spectacular solvatochromic reversal behavior observed for a stilbazolium merocyanine (SM) called Brooker's merocyanine dye. This...
The dimethylamino nitro stilbene (DANS) molecule is studied for exploring solvent effects on two-photon absorption using the quantum mechanical/molecular mechanical (QM/MM) response theory...
Spurred by the pioneering modeling studies of Sylvio Canuto on absorption spectra and solvatochromic shifts of organic molecules in polar and nonpolar solvents, we report in this work a...
We present results of molecular dynamics (MD) simulations of a double-stranded DNA fragment of sequence 5'-d(CGCGAGTTCGCG)-3' and 3'-d(GCGCTCAAGCGC)-5' in its native form and altered with guanine...
We present an adaptive finite element method for the compressible Euler equations, based on a posteriori error estimation of a quantity of interest in terms of a dual problem for the linearized...
We consider element-by-element Schur complement approximations for indefinite and general nonsymmetric matrices of two-by-two block form, as arising in finite element discretized systems of PDEs....
We describe how membrane proteins diffuse laterally in the membrane plane together with the lipids surrounding them. We find a number of intriguing phenomena. The lateral displacements of the...
A new biobanking method is proposed, wherein samples and associated data would be deposited anonymously and labelled using a PIN code that is produced on the basis of personal biological...
Statins are potent lipid-lowering drugs but anti-inflammatory effects have also been suggested. Our aim was to investigate the effects of simvastatin on proinflammatory cytokines and matrix...
Ionisation equilibria in proteins are influenced by conformational flexibility, which can in principle be accounted for by molecular dynamics simulation. One problem in this method is the bias...
In order to study the role of surface ligands in determining optical properties of colloidal quantum dots (QDs), we have selectively fabricated and studied CdSe/CdS core-shell QDs with strongly...
In this paper, we have synthesized a series of core/shell quantum dots (QDs) for the purpose of enhancing the electron transfer from the dots to a TiO(2) substrate. We make use of the fact that...
Type-II quantum dots (QDs) were applied for QDs-sensitized solar cells for the first time and showed prominent absorbed photon to current conversion efficiency.
O 1s, C 1s, and S 2p core-valence double ionization electron spectra of the OCS molecule have been obtained experimentally by a time-of-flight photoelectron-photoelectron coincidence spectroscopy...
We have performed relativistic calculations of single and double core 1s hole states of the noble gas atoms in order to explore the relativistic corrections and their additivity to the ionization...
This paper reports a study of valence photoionization of the LiCl monomer and dimer. The behavior of the photoionization partial cross section for molecular valence orbitals was measured as a...
The development of electronic response theory in quantum chemistry has been reviewed, starting from the early 1970's and reaching the current state-of-the-art. The general theory has been applied...
Working memory capacity is usually measured as the number of stimuli correctly remembered. However, these measures lack precision when assessing individuals with low capacity. This study aimed to...
Fluid intelligence (Gf) predicts performance on a wide range of cognitive activities, and children with impaired Gf often experience academic difficulties. Previous attempts to improve Gf have...
Background: Phase contrast cardiovascular magnetic resonance (CMR) is able to measure all three directional components of the velocities of blood flow relative to the three spatial dimensions and...
The objective of this study is to develop models for the subgrid-scale (SGS) stress and the SOS scalar flux by applying the same kind of methodology that leads to the explicit algebraic Reynolds...
The dynamical and thermodynamic stability of a single monolayer of SiN(x) sandwiched isostructurally between B1-TiN(001) and (111) oriented slabs are investigated by means of density functional...
Short laminar separation bubbles can develop on a flat plate due to an externally imposed pressure gradient. Here, these bubbles are computed by means of direct numerical simulations. Laminar-...
It has been shown that the Earth's inner core has an axisymmetric anisotropic structure with seismic waves traveling similar to 3% faster along polar paths than along equatorial directions....
OBJECTIVES: Since there are clear indications that schizophrenia is a systemic disorder, we sought for a common molecular basis for schizophrenia abnormalities in brain and body. Our hypothesis...
Bcl-xL is an antiapoptotic member of the Bcl-2 protein family and an attractive target for the development of anticancer agents. Here we describe the isolation of binders to Bcl-xL from a DNA-...
OBJECTIVE: The goal was to describe the temporal pattern of neonatal plasma glucose levels and associations with maternal glucose levels, cord serum C-peptide levels, and neonatal size and...
Harvesting energy directly from sunlight using photovoltaic technology is an essential component of the future global energy production programmes (A. Hagfeldt and M. Gratzel, Molecular...
The effective solvent-mediated potentials for Na(+) and Cl(-) ions in aqueous solution were calculated in a wide range of temperatures from 0 to 100 degrees C. The potentials have been determined...
Saturn's moon Titan exhibits an active weather cycle that involves methane(1-8). Equatorial and mid-latitude clouds can be organized into fascinating morphologies on scales exceeding 1,000 km (ref...
We use direct numerical simulations of forced MHD turbulence with a forcing function that produces two different signs of kinetic helicity in the upper and lower parts of the domain. We show that...
Introduction: The development of atherosclerotic plaques has been associated with the patterns of wall shear stress (WSS). However, much is still uncertain with the methods used to calculate WSS....
Coherent anti-Stokes Raman scattering (CARS) of the 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) C(3)H(6)N(6)O(6) molecule is studied by ab initio methods. The results are compared to available...
In order to investigate structural and dynamical properties of local anesthetic articaine in a model lipid bilayer, a series of molecular dynamics simulations have been performed. Simulations were...
The peculiar bonding situation in gamma boron is characterized on the basis of an experimental electron-density distribution which is obtained by multipole refinement against low-temperature...
The global linear stability of the flat-plate boundary-layer flow to three-dimensional disturbances is studied by means of an optimization technique. We consider both the optimal initial condition...
We determine the initial condition on the laminar-turbulent boundary closest to the laminar state using nonlinear optimization for plane Couette flow. Resorting to the general evolution criterion...
The Gaussian beam superposition method is an asymptotic method for computing high frequency wave fields in smoothly varying inhomogeneous media. In this paper we study the accuracy of the Gaussian...
Royal jelly (RJ) excreted by honeybees and used as a nutritional and medicinal agent has estrogen-like effects, yet the compounds mediating these effects remain unidentified. The possible effects...
Cys-loop receptors constitute a superfamily of ion channels gated by ligands such as acetylcholine, serotonin, glycine, and gamma-aminobutyric acid. All of these receptors are thought to share...
The present work addresses the solvatochromic shift of phenol blue (PB) dye. For this purpose the results of Car-Parrinello molecular dynamics (CPMD) simulations for PB in gas phase are compared...
We have investigated the dependence of the static first hyperpolarizability on the bond-length alternation (BLA) parameter. Our analysis indicates that the validity of the first...
Multilayers of combinations of NiO, Ni(3)N and Ni have been grown by ALD and CVD techniques at 250 degrees C. Layers of low thermodynamical stability have been modified to reach the target...
A spectrally accurate method for the fast evaluation of N-particle sums of the periodic Stokeslet is presented. Two different decomposition methods, leading to one sum in real space and one in...
A spectrally accurate fast method for electrostatic calculations under periodic boundary conditions is presented. We follow the established framework of FFT-based Ewald summation, but obtain a...
Recently, Lovejoy et al. (2009) argued that the steep similar to k(-3) atmospheric kinetic energy spectrum at synoptic scales (greater than or similar to 1000km) observed by aircraft is a spurious...
We carry out three high resolution direct numerical simulations of the two-dimensional Navier-Stokes equation to test Batchelor's similarity hypotheses of an equilibrium spectral range and an...
We have evaluated the performance of two classes of probabilistic models for substitution rate variation over phylogenetic trees. In the first class, branch rates are considered to be independent...
In many applications of Direct Volume Rendering (DVR) the importance of a certain material or feature is highly dependent on its relative spatial location. For instance, in the medical diagnostic...
The paracellular space defines the passive permeation of hydrophilic compounds in epithelia. The goal of this study was to characterise the paracellular permeation pathway in the human intestinal...
We study the role of propagation of strong x-ray free-electron laser pulses on the Auger effect. When the system is exposed to a strong x-ray pulse the stimulated emission starts to compete with...
In parallel with the proliferation of ontologies and their use in semantically-enabled applications, the issue of finding and dealing with defects in ontologies has become increasingly important....
The uptake of carbon dioxide and nitrogen gas by zeolite NaKA was studied. A very high ideal CO(2)-over-N(2) selectivity and a high CO(2) capacity were observed at an optimal K(+) content of 17 at...
Ontologies are recognized as a key technology for semantics-based integration of the many available biomedical data sources. However, developing ontologies is not an easy task and the resulting...
Despite the central role of estrogen exposure in breast and endometrial cancer development and numerous studies of genes in the estrogen metabolic pathway, polymorphisms within the pathway have...
The effects of laser irradiation on the surface microstructure and optical properties of ZnO films deposited on glass substrates were investigated experimentally and compared with those of thermal...
The vertical structure of gas-phase dimethyl sulphide [DMS(g)] in the high Arctic atmosphere is investigated during a summer season. The model results show that the near-surface DMS(g)...
Attractor neural networks are thought to underlie working memory functions in the cerebral cortex. Several such models have been proposed that successfully reproduce firing properties of neurons...
Changes in oscillatory brain activity are strongly correlated with performance in cognitive tasks and modulations in specific frequency bands are associated with working memory tasks. Mesoscale...
Medical imaging plays a central role in a vast range of healthcare practices. The usefulness of 3D visualizations has been demonstrated for many types of treatment planning. Nevertheless, full...
In recent years, there has been increased interest in carbon cycling in natural systems due to its role in a changing climate. Northern latitude systems are especially important as they may serve...
Permafrost influences the hydrologic response of a catchment. In this study, we test the ability of recession flow analysis to reflect thawing of permafrost at the catchment scale for the well-...
Background: High throughput pyrosequencing (454 sequencing) is the major sequencing platform for producing long read high throughput data. While most other sequencing techniques produce reading...
Systematic construction of coarse-grained molecular models from detailed atomistic simulations, and even from ab initio simulations is discussed. Atomistic simulations are first performed to...
Rapid development of computer power during the last decade has made molecular simulations of lipid bilayers feasible for many research groups, which, together with the growing general interest in...
The turbulent diffusivity tensor is determined for linear shear-flow turbulence using numerical simulations. For moderately strong shear, the diagonal components are found to increase...
The cell envelope of Escherichia coil is an essential structure that modulates exchanges between the cell and the extra-cellular milieu. Previous proteomic analyses have suggested that it contains...
We present comprehensive results on continuous atmospheric cluster and particle measurements in the size range similar to 1-42 nm within the European Integrated project on Aerosol Cloud Climate...
More than a hundred biochemical species, activated by neurotransmitters binding to transmembrane receptors, are important in long-term potentiation (LTP) and long-term depression (LTD). To...
Molecular dynamics simulations of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 have been performed and analysed with respect to...
The impact of surface flux boundary conditions and geostrophic forcing on multiday evolution of flow in the atmospheric boundary layer (ABL) was assessed using large-eddy simulations (LES). The...
P>Background: Myocardial dynamics are three-dimensional (3D) and time-varying. Cineradiography of surgically implanted makers in animals or patients is accurate for assessing these events, but...
Herein, we use first principles calculations to study the energy of the (11 (2) over bar1) twin boundary in Zr, Zn, Mg, Ti, and Be. This boundary is important for understanding the microyielding...
In our paper, we show that carbonates can be formed with almost no energetic barrier from CO(2) and metal-oxide binuclear MO(x)M species (M = Mg, Ca, Sr, Ba, with X = 1-4, depending on the cation...
Implicit solvent representations, in general, and generalized Born models, in particular, provide an attractive way to reduce the number of interactions and degrees of freedom in a system. The...
High-performance implementations of molecular dynamics (MD) simulations play an important role in the study of macromolecules. Recent advances in both hardware and simulation software have...
Multiple templates can often be used to build more accurate homology models than models built from a single template. Here we introduce PconsM, an automated protocol that uses multiple templates...
We review methods to compute X-ray absorption spectra (XAS) with special focus on the transition-potential approach of Triguero et al. [Phys. Rev. B 58 (1998) 8097] and its application to...
Methods This article presents a method for correcting the bias in FR estimates from such misclassification of family history, using a simple formula that depends on the prevalence and sensitivity...
Vitamin D may influence blood pressure through the renin-angiotensin system, parathyroid hormone levels, myocardial function, inflammation, and vascular calcification. In the past several years, a...
A cost-efficient way to increase power in a genetic association study is to pool controls from different sources. The genotyping effort can then be directed to large case series. The Nordic...
Introduction: Several studies have examined the effect of genetic variants in genes involved in the estrogen metabolic pathway on mammographic density, but the number of loci studied and the...
Introduction: Although a role of childhood body size in postmenopausal breast cancer risk has been established, less is known about its influence on tumour characteristics. Methods: We studied the...
Introduction: Breast cancer is a heterogeneous disease and may be characterized on the basis of whether estrogen receptors (ER) are expressed in the tumour cells. ER status of breast cancer is...
In an attempt to identify common disease susceptibility alleles for breast cancer, we performed a combined analysis of three genome-wide association studies (GWAS), involving 2,702 women of...
Introduction: Breast cancer is a complex disease and may be sub-divided into hormone-responsive (estrogen receptor (ER) positive) and non-hormone-responsive subtypes (ER-negative). Some evidence...
The present study investigates the effects of ambient free-stream turbulence (FST) on the momentum and heat transfer in a spatially developing, turbulent flat-plate boundary layer via large-eddy...
Water vapor in the atmosphere can condensate and form cloud droplets when there is a certain amount of humidity and a presence of cloud condensation nuclei, and organic solutes called surfactants...
Aerosol particles in the atmosphere are important participants in the formation of cloud droplets and have significant impact on cloud albedo and global climate. According to the Kohler theory...
Metal ions play essential roles in biological processes and have attracted much attention in both experimental and theoretical fields. By using the molecular dynamics simulation technology, we...
The photochromic iridium(III) complex (Py-BTE)(2)Ir(acac) synthesized by Tan et al. [W. Tan et al., Org. Lett. 2009, 11, 161-164] has shown distinct photo-reactivity and photo-controllable...
Linear and quadratic response time-dependent density functional theory is applied to study the photophysical properties of iridium complexes with phenylisoquinoline and phenylpyridine ligands. The...
Time-dependent density functional theory (TD-DFT) with linear and quadratic response approaches was applied to calculate absorption and luminescence spectra of a number of facial and meridional...
Introduction: Given the role of estrogen in breast carcinogenesis and the modification of estrogen receptor (ER) activity by its biochemical cofactors, we hypothesize that genetic variation within...
Background: The orderly progression through mitosis is regulated by the Anaphase-Promoting Complex (APC), a large multiprotein E(3) ubiquitin ligase that targets key cell-cycle regulators for...
A presentation of the complex polarization propagator in the restricted open-shell self-consistent field approximation is given. It rests on a formulation of a resonant-convergent, first-order...
Self-consistent convective dynamo simulations in wedge-shaped spherical shells are presented. Differential rotation is generated by the interaction of convection with rotation. Equatorward...
Angular momentum transport due to hydrodynamic turbulent convection is studied using local three-dimensional numerical simulations employing the shearing box approximation. We determine the...
In this study, the mean and variability of boundary layer height (BLH) are analyzed along a transect in the eastern Pacific Ocean for the summer of 2003 using BLH estimates based on the height of...
This study has identified and mapped the occurrences of three different types of climate-driven and hydrologically mediated regime shifts in inland Arctic ecosystems: (i) from tundra to shrubland...
We investigate the influence of clouds on the surface energy budget and surface temperature in the sea-ice covered parts of the ocean north of the Arctic circle in present-day climate in nine...
Membrane fusion is essential to both cellular vesicle trafficking and infection by enveloped viruses. While the fusion protein assemblies that catalyze fusion are readily identifiable, the...
Membrane interfaces are critical to many cellular functions, yet the vast array of molecular components involved make the fundamental physics of interaction difficult to define. Water has been...
The response equations as occurring in the Hartree-Fock, multiconfigurational self-consistent field, and Kohn-Sham density functional theory have identical matrix structures. The algorithms that...
We have determined the optimal placement of individual transmembrane helices in the Pyrococcus horikoshu Glt(Ph) glutamate transporter homolog in the membrane. The results are in close agreement...
In many practical multiphase flow problems, i.e. treatment of gas emboli and various microfluidic applications, the effect of interfacial surfactants, or surface reacting agents, on the surface...
In this paper an efficient method to study sound generation processes in low Mach number flows is presented. We apply the methodology on a two-dimensional flow over a cavity with smoothed corners...
Acoustic wave propagation in flow ducts is commonly modeled with time-domain non-linear Navier-Stokes equation methodologies. To reduce computational effort, investigations of a linearized...
Left ventricular myofibers are connected by an extensive extracellular collagen matrix to form myolaminar sheets. Histological cardiac tissue studies have previously observed a pleated transmural...
In order to optimize the vane film cooling and thereby increase the efficiency of a gas turbine, different film cooling configurations were experimentally investigated. Dynamic similarity was...
State-of-the-art climate models were used to simulate climate conditions in Europe during Greenland Stadial (GS) 12 at 44 ka BP. The models employed for these simulations were: (i) a fully coupled...
Modal and non-modal linear stability analysis of channel flow with a dilute particle suspension is presented where particles are assumed to be solid, spherical, and heavy. The two-way coupling...
The physical mechanism of the folding and unfolding of chromatin is fundamentally related to transcription but is incompletely characterized and not fully understood. We experimentally and...
The paper reviews our current studies on the experimentally induced cation compaction and aggregation in solutions of DNA and nucleosome core particles and the theoretical modelling of these...
Synaptic plasticity is thought to underlie learning and memory, but the complexity of the interactions between the ion channels, enzymes and genes that are involved in synaptic plasticity impedes...
Prostate cancer (PrCa) is the most frequently diagnosed male cancer in developed countries. We conducted a multi-stage genome-wide association study for PrCa and previously reported the results of...
Unreliable rainfall may be a main cause of poverty in rural areas, such as the Kisumu district by Lake Victoria in Kenya. Climate change may further increase the negative effects of rainfall...
Objective-Hepatocyte nuclear factor-4 alpha (HNF4A) is a transcription factor that influences plasma triglyceride metabolism via an as of yet unknown mechanism. In this study, we searched for the...
In this paper we study the comprehensive effects on volume rendered images due to numerical errors caused by the use of finite precision for data representation and processing. To estimate actual...
Magnetic helicity has risen to be a major player in dynamo theory, with the helicity of the small-scale field being linked to the dynamo saturation process for the large-scale field. It is a...
The description of chemical reactions by means of quantum mechanical methods is an important task and gets even more challenging if excited states have to be considered. This work focuses on the...
Limited bandwidth to off-chip main memory is a performance bottleneck in chip multiprocessors for streaming computations, such as Cell/B.E., and this will become even more problematic with an...
Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with...
European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the...
A synthetic strategy was developed for the preparation of porphyrins containing between one and four stereogenic centers, such that their molecular weights vary only as a result of methyl groups...
Reduced-order models of the nonlinear complex Ginzburg-Landau (CGL) equation are computed using a nonlinear generalization of balanced truncation. The method involves Galerkin projection of the...
Background: In water-soluble proteins it is energetically favorable to bury hydrophobic residues and to expose polar and charged residues. In contrast to water soluble proteins, transmembrane...
High-pressure homogenizers (HPHs) are used to create sub-micron emulsions in low-viscosity fluids. As the flow in a real HPH is very extreme, with gaps ranging from 10 to 100 pm and high...
Alzheimer's disease (AD) pathogenesis is associated with formation of amyloid fibrils caused by polymerization of the amyloid beta-peptide (A beta), which is a process that requires unfolding of...
The aim of the present paper is to obtain a better understanding of the stability properties of wakes generated by wind turbine rotors. To accomplish this, a numerical study on the stability of...
To investigate the performance of postmortem magnetic resonance imaging (pmMRI) in identification and characterization of lethal myocardial infarction in a non-invasive manner on human corpses....
A quantification of T1, T2, and PD in high isotropic resolution was performed on corpses. Isotropic and quantified postmortem magnetic resonance (IQpmMR) enables sophisticated 3D postprocessing,...
The changes in force characteristics as well as the shedding patterns for various dual sphere configurations are studied. The Reynolds numbers considered are 300, 600 and two different inflow...
Charge transport in conjugated polymers has been investigated using Monte Carlo simulations implemented on top of the Marcus theory for donor-acceptor transition rates. In particular, polaron...
This study investigated the diurnal cycle of precipitation in Sweden using hourly ground observations for 1996-2008. General characteristics of phase and amplitude for the diurnal cycle of...
In this paper we present a novel algorithm for improving the visibility of surveillance videos degraded by fog and/or rain. The proposed algorithm adaptively enhances the global and local contrast...
Background: Many parasites use multicopy protein families to avoid their host's immune system through a strategy called antigenic variation. RIFIN and STEVOR proteins are variable surface antigens...
Two large gene and protein superfamilies, SDR and MDR (short- and medium-chain dehydrogenases/reductases), were originally defined from analysis of alcohol and polyol dehydrogenases. The...
Background: Reverse transcriptase is a major drug target in highly active antiretroviral therapy (HAART) against HIV, which typically comprises two nucleoside/nucleotide analog reverse...
We constructed an accurate polyether force field for implicit solvent (IS) molecular dynamics (MD) simulations that matches local and global conformations of 1,2-dimethoxy-ethane (DME) and...
The short-chain dehydrogenase/reductase (SDR) superfamily now has over 47 000 members, most of which are distantly related, with typically 20-30% residue identity in pairwise comparisons, making...
Motivated by the locomotion of flagellated micro-organisms and by recent experiments of chemically driven nanomachines, we study the dynamics of bodies of simple geometric shape that are propelled...
Protein adsorption onto implant surfaces is of great importance for the regulation of implant bioactivity. Surface modification of implants is a promising way in the molecular design of...
Cavitation is common in high-pressure homogenizers, and has severe negative effects such as noise and mechanical wear, but may also have a beneficial effect in promoting fragmentation. Greater...
Particle image velocimetry is performed on a model of a high pressure homogenizer, scaled for qualitative similarity of the one phase turbulent flow field in a production scale homogenizer. Flow...
We report a classical interatomic force field for TiO2, which has been parametrized using density functional theory forces, energies, and stresses in the rutile crystal structure. The reliability...
A gradient-based optimization method for minimization of the total drag of an airfoil is presented. The viscous drag is minimized by delaying the laminar-turbulent transition. The gradients are...
Accurate functional measurement in cardiovascular diseases is important as inaccuracy may compromise diagnostic decisions. Cardiac function can be assessed using displacement encoding with...
Molecular chromophores with twisted pi-electron systems have been shown to possess unprecedented values of the quadratic hyperpolarizability, beta, with very large real parts and much smaller...
Cloud condensation nuclei act as cores for water vapour condensation, and their composition and chemical properties may enhance or depress the ability for droplet growth. In this study we use...
In mammalian cells, most integral membrane proteins are initially inserted into the endoplasmic reticulum membrane by the so-called Sec61 translocon. However, recent predictions suggest that many...
Predictions of future climate change have triggered a search for ways to reduce the release of greenhouse gases into the atmosphere. Carbon capture and storage (CCS) assists this goal by reducing...
Background: The Medium-chain Dehydrogenases/Reductases (MDR) form a protein superfamily whose size and complexity defeats traditional means of subclassification; it currently has over 15000...
Laminar flow control by suction of crossflow-dominated laminar-turbulent transition at Mach 2 was studied experimentally and numerically as part of the EU project SUPERTRAC. The measurements were...
Alcohol dehydrogenase 3 (ADH3) has been assigned a role in nitric oxide homeostasis due to its function as an S-nitrosoglutathione reductase. As altered S-nitrosoglutathione levels are often...
State-of-the-art methods for topology of alpha-helical membrane proteins are based on the use of time-consuming multiple sequence alignments obtained from PSI-BLAST or other sources. Here, we...
Many alpha-helical membrane proteins contain internal symmetries, indicating that they might have evolved through a gene duplication and fusion event Here, we have characterized internal...
Background: With the wealth of genomic data available it has become increasingly important to assign putative protein function through functional transfer between orthologs. Therefore, correct...
This paper presents a novel technique to efficiently compute illumination for Direct Volume Rendering using a local approximation of ambient occlusion to integrate the intensity of incident light...
We propose a resolution of d'Alembert's Paradox comparing observation of substantial drag/lift in fluids with very small viscosity such as air and water, with the mathematical prediction of zero...
In this paper we first review our recent work on a new framework for adaptive turbulence simulation: we model turbulence by weak solutions to the Navier-Stokes equations that are wellposed with...
In this paper, we describe an incompressible Unified Continuum(UC) model in Euler (laboratory) coordinates with a moving mesh for tracking the fluid-structure interface as part of the...
Objective: To investigate the validity and reproducibility of a newly developed internet-based self-administered hearing test using clinical pure-tone air-conducted audiometry as gold standard....
Despite its long history of use and abuse in human culture, the molecular basis for alcohol action in the brain is poorly understood. The recent determination of the atomic-scale structure of GLIC...
In this work we highlight the potential of NEXAFS-near-edge X-ray absorption fine structure-analysis to perform refinements of hydrogen-bond structure in DNA. For this purpose we have carried out...
Near edge x-ray absorption fine-structure spectra of graphenes are calculated using hybrid density-functional theory with the equivalent core hole approximation, aiming to resolve the ongoing...
In the present work, we have undertaken a combined experimental and theoretical study of X-ray spectroscopies for DNA base pairs, more precisely near-edge X-ray absorption, X-ray emission, and...
We have studied the lattice stability of face centred cubic (fcc) versus hexagonal close packed (hcp) Fe-Mn random alloys using ab initio calculations. In the calculations we considered the...
We have studied the influence of Al and Si additions on the elastic properties of face-centered cubic (fcc) Fe-Mn random alloys with Fe/Mn ratios of 4.00 and 2.33 using ab initio calculations....
We investigate several existing interface procedures for finite difference methods applied to advection-diffusion problems. The accuracy, stiffness and reflecting properties of various interface...
New technologies to generate high-dimensional data provide unprecedented opportunities for unbiased identification of biomarkers that can be used to optimize pre-operative planning, with the goal...
Background: The stability of atherosclerotic plaques determines the risk for rupture, which may lead to thrombus formation and potentially severe clinical complications such as myocardial...
Permafrost responses to a changing climate can affect hydrological and biogeochemical cycling, ecosystems and climate feedbacks. We have simulated a model permafrost system in the temperature...
The formulation vehicle Cremophor EL has previously been shown to affect paclitaxel kinetics, but it is not known whether it also affects the kinetics of paclitaxel metabolites. This information...
Fredriksson AG, Zajac J, Eriksson J, Dyverfeldt P, Bolger AF, Ebbers T, Carlhall CJ. 4-D blood flow in the human right ventricle. Am J Physiol Heart Circ Physiol 301: H2344-H2350, 2011. First...
P>The cystatin family comprises a group of generally broadly expressed protease inhibitors. The Cres/Testatin subgroup (CTES) genes within the type 2 cystatins differs from the classical type 2...
Impact ionization and Auger recombination in nanoscale spherical quantum dots (QDs) have been Studied theoretically. It is shown that due to the strong quantum confinement of both electrons in the...
The expression of plant shikimate kinase (SK; EC 2.7.1.71), an intermediate step in the shikimate pathway to aromatic amino acid biosynthesis, is induced under specific conditions of environmental...
Based on first principles calculations, we propose a solubility control method of magnetic impurities in dilute magnetic semiconductors (DMSs). The low solubility of Mn in (Ga, Mn)As is...
We performed molecular simulations to study ion pairing in aqueous solutions. Our results indicate that ion specific interactions of Li(+), Na(+), and K(+) with the dimethyl phosphate anion are...
Large eddy simulation was applied for flow of Re = 2000 in a stenosed pipe in order to undertake a thorough investigation of the wall shear stress (WSS) in turbulent flow. A decomposition of the...
We show that the anisotropy of the recoil velocity distribution of x-ray-ionized atoms or molecules leads to observable splittings in subsequent optical fluorescence or absorption when the...
Recent cloud-resolving model studies of single (isolated) deep convective clouds have shown contradicting results regarding the response of the deep convection to changes in the aerosol...
For large regions of many proteins, and even entire proteins, no homology to known domains or proteins can be detected. These sequences are often referred to as orphans. Surprisingly, it has been...
Under cooling, a liquid can undergo a transition to the glassy state either as a result of a continuous slowing down or by a first-order polyamorphous phase transition. The second scenario has so...
We have studied the partitioning of amphiphilic peptides at the air-water interface. The free energy of adsorption from bulk to interface was calculated by determining the potential of mean force...
Peptides are highly promising building blocks for design and development of novel materials with potential application areas ranging from drug design to biotechnology. The necessity to understand...
This paper presents a new directional multilevel algorithm for solving N-body or N-point problems with highly oscillatory kernels. We address the problem by first proving that the interaction...
Multi-scale wave propagation problems are computationally costly to solve by traditional techniques because the smallest scales must be represented over a domain determined by the largest scales...
The aerosol optical depth has in several recent studies been found to correlate with cloud fraction. This study examines the global distribution of the total correlation between aerosol optical...
We present SkePU, a C++ template library which provides a simple and unified interface for specifying data-parallel computations with the help of skeletons on GPUs using CUDA and OpenCL. The...
Background: Several bioinformatic approaches have previously been used to find novel sites of ADAR mediated A-to-I RNA editing in human. These studies have discovered thousands of genes that are...
In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a...
Eriksson J, Dyverfeldt P, Engvall J, Bolger AF, Ebbers T, Carlhall CJ. Quantification of presystolic blood flow organization and energetics in the human left ventricle. Am J Physiol Heart Circ...
Background: One of the most well described cellular processes is the cell cycle, governing cell division. Mathematical models of this gene-protein network are therefore a good test case for...
Background. The diagnostic value of non-invasive methods for diagnosing renal artery stenosis in patients with renal insufficiency is incompletely known. Methods. Forty-seven consecutive patients...
A procedure to locally change the order of accuracy of finite difference schemes is developed. The development is based on existing Summation-By-Parts operators and a weak interface treatment. The...
The exact role of fluid mechanics in the patho-physiological process of atherosclerosis has been a research topic over many years, yet without clear conclusive result. One has observed that...
The secondary motion induced by flow through curves and bifurcations has been subject to investigation over long time due to its importance in physiological and technological applications. In...
Pulsating flow through bifurcations are of general interest. In the human body such flows are also very common; for example in blood vessels and the respiratory tract. The characteristics of the...
In this paper, the availability of Detached-Eddy Simulations (DES) for simulating unsteady crosswind aerodynamics in industrial applications is explored and reported. The flow around a simple car...
Feature hierarchies are essential to many visual object recognition systems and are well motivated by observations in biological systems. The present paper proposes an algorithm to incrementally...
In this paper, we present a novel scheme for anisotropic diffusion driven by the image autocorrelation function. We show the equivalence of this scheme to a special case of iterated adaptive...
Tumor necrosis factor (TNF) and interleukin 10 (IL10) are promising candidate susceptibility genes for non-Hodgkin lymphoma (NHL). Chromosomal translocation breakpoint genes are of interest, given...
Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important...
Background: Truncating mutations in ATM have been shown to increase the risk of breast cancer but the effect of missense variants remains contentious. Methods: We have genotyped five polymorphic (...
Background: As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog...
Orthology is one of the most important tools available to modern biology, as it allows making inferences from easily studied model systems to much less tractable systems of interest, such as...
Methods This conceptual article describes the origins, purpose and scientific foundations of the DataSHaPER (DataSchema and Harmonization Platform for Epidemiological Research;...
The phase stability of Ti(2)AlC upon oxygen incorporation has been studied by means of first-principles calculations. Recent experimental observations of this so-called MAX phase (M=early...
Human papillomaviruses (HPV) are established as a major cause of cervical carcinoma. However, causality inference is dependent on prospective evidence showing that exposure predicts risk for...
The controlled preparation of chiral structures is a contemporary challenge for supramolecular science because of the interesting properties that can arise from the resulting materials, and here...
Genetic variation in the androgen-to-estrogen conversion pathway has been shown to be associated with risk of breast cancer and, in particular, with estrogen receptor (ER) positive tumours. We...
Taking disease subtypes into account when testing for an association between genetic factors and disease risk may help to identify specific aetiologic pathways. One way to assess a genetic...
This study has investigated and outlined the possible quantification and mapping of the distributions of advective solute travel times through hydrological catchments. These distributions are...
Advective solute travel times and their distributions in hydrological catchments are useful descriptors of the dynamics and variation of the physical mass transport among and along the different...
The melting point for the tetragonal and cubic phases of zirconia (ZrO2) was computed using Z-method microcanonical molecular dynamics simulations for two different interaction models: the...
Spin restricted open-shell Density Functional Theory calculations have been carried out by means of linear response theory to investigate the visible absorption spectrum of copper(II)...
Specific and basicity solvent effects on the visible near-infrared electronic transitions and the electron paramagnetic resonance (EPR) parameters of the copper(II) acetylacetonate complex, Cu(...
Background: Computed tomography (CT) is becoming increasingly popular as a non-invasive method for visualizing the coronary arteries but patient radiation doses are still an issue. Postprocessing...
This study has quantified the regional evaporation and evapotranspiration changes, and the associated latent heat flux and surface temperature changes in the Central Asian region of the Aral Sea...
This study develops a general quantification framework for consistent intermodel and intercatchment comparison of the nutrient and pollutant mass loading from multiple sources in a catchment area...
The Energy Committee of the Royal Swedish Academy of Sciences has in a series of projects gathered information and knowledge on renewable energy from various sources, both within and outside the...
MUSIC is a standard API allowing large scale neuron simulators to exchange data within a parallel computer during runtime. A pilot implementation of this API has been released as open source. We...
This paper presents a model, using a phase-field method, that is able to simulate the motion of a solid sphere impacting on a liquid surface, including the effects of capillary and hydrodynamic...
This paper presents a technology for dispensing droplets through thin liquid layers. The system consists of a free liquid film, which is suspended in a frame and positioned in front of a...
The relative importance of regional processes inside the Arctic climate system and the large scale atmospheric circulation for Arctic interannual climate variability has been estimated with the...
To identify weather controls of beech diameter growth and masting in southern Sweden, we analyze records of monthly weather, regional masting record, and tree-ring chronologies from five beech-...
For parallel shear flows, transition to turbulence occurs only for perturbations of sufficiently large amplitude. It is therefore relevant to study the shape, amplitude, and dynamics of the least...
The formation of turbulent patterns in plane Couette flow is investigated near the onset of transition, using numerical simulation in a very large domain of size 800 h x 2h x 356 h. Based on a...
We present for the first time a complete bifurcation diagram of plane Couette flow based on direct numerical simulation of the full Navier-Stokes equations. The use of an unusually large...
We present an integrated and updated quantitative estimation of the river discharge and the meltwater flux and mass contributions from glaciers to the Arctic Ocean and to sea level rise. The...
Purpose: To investigate the utility of MRI measurement of left atrial (LA) flow patterns and turbulent kinetic energy (TKE) in patients with clinically significant mitral regurgitation. Materials...
MRI can measure several important hemodynamic parameters but might not yet have reached its full potential. The most common MRI method for the assessment of flow is phase-contrast MRI velocity...
To study the effects of water on conformational dynamics of polyalcohols, Molecular Dynamics simulations of glycerol water liquid mixtures have been carried out at different concentrations: 42.9...
In magnetic alloys, the effect of finite temperature magnetic excitations on phase stability below the Curie temperature is poorly investigated, although many systems undergo phase transitions in...
Background: The omics fields promise to revolutionize our understanding of biology and biomedicine. However, their potential is compromised by the challenge to analyze the huge datasets produced....
Direct numerical simulations and mean-field theory are used to model reactive front propagation in a turbulent medium. In the mean-field approach, memory effects of turbulent diffusion are taken...
We determine the magnetic helicity, along with the magnetic energy, at high latitudes using data from the Ulysses mission. The data set spans the time period from 1993 to 1996. The basic...
Atomic resolution and coarse-grained simulations of dimyristoylphosphatidylcholine lipid bilayers were analyzed for fluctuations perpendicular to the bilayer using a completely Fourier-based...
The decay of fluctuations in fluid biomembranes is strongly stretched and nonexponential on nanometer lengthscales. We report on calculations of structural correlation functions for lipid bilayer...
Non-modal analysis determines the potential for energy amplification in stable flows. The latter is quantified in the frequency domain by the singular values of the resolvent operator. The present...
The traditional method for extracting electron density and other transmembrane profiles from molecular dynamics simulations of lipid bilayers fails for large bilayer systems, because it assumes a...
Numerical simulations are used to study the vertical dispersion of fluid particles in homogeneous turbulent flows with a stable stratification. The results of direct numerical simulations are in...
Rapid changes to the Arctic hydrological cycle challenge both our process understanding and our ability to find appropriate adaptation strategies. We have investigated the relevance and accuracy...
Breast cancers demonstrate substantial biological, clinical and etiological heterogeneity. We investigated breast cancer risk associations of eight susceptibility loci identified in GWAS and two...
In this article, we present a methodological framework that meets novel requirements emerging from upcoming types of accelerated and highly configurable neuromorphic hardware systems. We describe...
Phase diagrams of refractory metals remain essentially unknown. Moreover, there is an ongoing controversy over the high-pressure melting temperatures of these metals: results of diamond anvil cell...
Recent paleoclimate proxy reconstructions show that tropical surface temperatures may have been as high as 35 degrees-40 degrees C in the Early Cenozoic. Here, we study the tropical atmospheric...
Magnetic helicity fluxes are investigated in a family of gauges in which the contribution from ideal magnetohydrodynamics takes the form of a purely advective flux. Numerical simulations of...
In the present paper we present a phenomenological description of droplet dynamics in a bifurcating channel that is based on three-dimensional numerical experiments using the Phase Field theory....
Background: Predicting metabolic sites is important in the drug discovery process to aid in rapid compound optimisation. No interactive tool exists and most of the useful tools are quite expensive...
Four additional variants of alcohol and aldehyde dehydrogenases have been purified and functionally characterized, and their primary structures have been determined. The results allow conclusions...
Deep saline aquifers have large capacity for geological CO(2) storage, but are generally not as well characterized as petroleum reservoirs. We here aim at quantifying effects of uncertain...
Photoluminescent NaYF(4):Yb(3+)/Tm(3+) nanocrystals are ideally suited for in vitro and in vivo photoluminescence (PL) bioimaging due to their virtue of near-infrared to near-infrared (NIR-to-NIR...
We report intense upconversion photoluminescence (PL) In colloidal LiYF(4):Er(3+)nanocrystals under excitation with telecom-wavelength at 1490 nm. The intensities of two- and three-photon anti-...
We report core/shell NaYbF(4) : Tm(3+)/NaGdF(4) nanocrystals to be used as probes for bimodal near infrared to near infrared (NIR-to-NIR) upconversion photoluminescence (UCPL) and magnetic...
The present work addresses isotropic hyperfine coupling constants in polyatomic systems with a particular emphasis on a largely neglected, but a posteriori significant, effect, namely zero-point...
The CASSCF and CASPT2 methodologies have been used to explore the potential energy surfaces of lumisantonin in the ground and low-lying triplet states along the photoisomerization pathways....
In this paper. we identify and propose solutions for several issues encountered when designing a mesh adaptation package, such as mesh-to-mesh projections and mesh database design, and we describe...
To identify susceptibility loci for non-Hodgkin lymphoma subtypes, we conducted a three-stage genome-wide association study. We identified two variants associated with follicular lymphoma at 6p21....
The nonlinear stability of laminar sinuously bent streaks is studied for the plane Couette flow at Re = 500 in a nearly minimal box and for the Blasius boundary layer at Re(delta)(*)=700. The...
Lipid shape and charge are connected with the physical properties and the biological function of membranes. Cardiolipin, a double phospholipid with four chains and the potential of changing its...
Cardiolipin is a key lipid component in many biological membranes. Proton conduction proton-lipid interactions on the membrane surface are thought to be central to mitochondrial energy production...
We have carried out molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome, to study the effect of the common tRNA modifications cmo(5)U34 and m(6)A37. In tRNA(...
Studying gene-environment interactions requires that the amount and quality of the lifestyle data is comparable to what is available for the corresponding genomic data. Sweden has several crucial...
Background: Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly...
Background: Improved glycaemic control during pregnancy in mothers with type 1 diabetes (T1DM) and gestational diabetes (GDM) has resulted in a marked reduction of perinatal mortality and...
Enhanced evapotranspiration (ET) over irrigated land and associated latent heat flux change can modify the climate. Model studies of such climate change effects of irrigation are commonly based on...
The parameter estimation variance of the Single Point Active Alignment Method (SPAAM) is studied through an experiment where 11 subjects are instructed to create alignments using an Optical See-...
The quantum chemical DFT method with the B3LYP hybrid functional in 6-31++G(d,p) and 6-311+G(d,p) basis sets is used to calculate the equilibrium geometric parameters of different conformations of...
Complexity of heterogeneous catchments poses challenges in predicting biogeochemical responses to human alterations and stochastic hydro-climatic drivers. Human interferences and climate change...
The large-scale dynamics of plasmas is well described within the framework of magnetohydrodynamics (MHD). However, whenever the ion density of the plasma becomes sufficiently low, the Hall effect...
Planetary albedo the reflectivity for solar radiation is of singular importance in determining the amount of solar energy taken in by the Earth-atmosphere system. Modeling albedo, and specifically...
The radiative flux perturbations and subsequent temperature responses in relation to the eruption of Mount Pinatubo in 1991 are studied in the ten general circulation models incorporated in the...
In this paper we prove stability of Robin solid wall boundary conditions for the compressible Navier-Stokes equations. Applications include the no-slip boundary conditions with prescribed...
The dynamics of a synthetic antiferromagnet (a metallic trilayer) have been explored and are shown to exhibit ultrafast switching on a time scale of tens of ps. This conclusion is based on first-...
Based on first-principles calculations and kinetic Monte Carlo simulations, we design a realistic and practical codoping technique for increasing the concentration of Mn atoms in GaAs and...
Ligand-gated ion channels (LGICs) significantly modulate anesthetic effects. Their exact molecular structure remains unknown. This has led to ambiguity regarding the proper amino acid alignment...
Background: Physical activity is associated with reduced risks of many chronic diseases. Data collected on physical activity in large epidemiological studies is often based on paper questionnaires...
The authors aimed to evaluate the web and an Interactive Voice Response (IVR) phone service as vehicles in population-based infectious disease surveillance. Fourteen thousand subjects were...
Background: Physical activity promotes health and longevity. Further elaboration of the role of physical activity for human health in epidemiological studies on large samples requires accurate...
BACKGROUND In 2008, we reported that radical prostatectomy, as compared with watchful waiting, reduces the rate of death from prostate cancer. After an additional 3 years of follow-up, we now...
The synthesis and the chiroptical properties of the two enantiomers of the hexacarboxylic acid cryptophane-A derivative, 1, are described in this article. The chiroptical and binding properties of...
Recent measurements of GaMnAs alloy samples with a very small content of P atoms prepared by ion-implanted pulsed laser melting (II-PLM) [Phys. Rev. Lett. 101, 087203 (2008)] have shown...
We present a coupled global climate model (CGCM) simulation, integrated for 1500 yr to quasi-equilibrium, of a stadial (cold period) within Marine Isotope Stage 3 (MIS 3). The simulated Greenland...
Using two- and three-dimensional hydromagnetic simulations for a range of different flows, including laminar and turbulent ones, it is shown that solutions expressing the field in terms of Euler...
In this study we provide the first numerical demonstration of the effects of turbulence on the mean Lorentz force and the resulting formation of large-scale magnetic structures. Using three-...
Some of the contributions of Chandrasekhar to the field of magnetohydrodynamics are highlighted. Particular emphasis is placed on the Chandrasekhar-Kendall functions that allow a decomposition of...
We outline recent developments of theoretical methodology for first-principles simulations of alloys at high pressure. Particular attention will be paid to the techniques for a treatment of...
We present calculations of structural and magnetic properties of the iron-pnictide superconductor LaFeAsO including electron-electron correlations. For this purpose we apply a fully charge self-...
We review results of recent combined theoretical and experimental studies of Ti(1-x)Al(x)N, an archetypical alloy system material for hard-coating applications. Theoretical simulations of lattice...
Nonlinear optimal perturbations leading to subcritical transition with minimum threshold energy are searched in the plane Poiseuille flow at Re = 1500. To this end we proceed in two steps. First a...
While overall hydrophobicity is generally recognized as the main characteristic of transmembrane (TM) alpha-helices, the only membrane system for which there are detailed quantitative data on how...
A new water-soluble cryptophane 1 derivative (penta-hydroxyl cryptophane-A) has been synthesized from cryptophanol-A and the chiroptical properties of its two enantiomers M M-1 and P P-1 have been...
ECD and NMR experiments show that the complexation of propylene oxide (PrO) within the cavity of an enantiopure water-soluble cryptophane 1 in NaOH solution is enantioselective and that the (R)-...
Tethered Lifting System (TLS) estimates of the dissipation rate of turbulent kinetic energy (epsilon) are reasonably well correlated with concurrent measurements of vertical velocity variance (...
We investigate the cooperative effects controlling the synthesis of a graphene nanoribbon on the Au(111) surface starting from an anthracene polymer using density functional calculations including...
Protein domain repeats are common in proteins that are central to the organization of a cell, in particular in eukaryotes. They are known to evolve through internal tandem duplications. However,...
The equation of state for hexagonal close packed (hcp or) phase of Fe at high pressure is created by employing molecular dynamics (MD) simulations in conjunction with the embedded atom method...
Recent laser-initiated strong shockwave measurements at Livermore provide the opportunity for verification of the MgO phase diagram at extreme pressures and temperatures. This calls for a...
Large scale molecular dynamics simulations of iron at high pressure and temperature are performed to investigate the physics of shear softening. A solid 16 x 10(6) atoms sample of iron is grown...
We have previously used molecular modeling and normal-mode analyses combined with experimental data to visualize a plausible model of a transmembrane ligand-gated ion channel. We also postulated...
We have calculated the equation of state and elastic properties of face-centered cubic Fe and Fe-rich Fe-Mg alloy at ultrahigh pressures from first principles using the Exact Muffin-Tin Orbitals...
We study the Fe/W(110) monolayer system through a combination of first-principles calculations and atomistic spin dynamics simulations. We focus on the dispersion of the spin-waves parallel to the...
CHARMM27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. We have here...
This paper presents an attempt to control the laminar-turbulent transition on a swept wine in supersonic flow The first part cleats with the control of the transition due to crossflow (CF)...
Double photoionization spectra of the CS2 molecule have been recorded using the TOF-PEPECO technique in combination with synchrotron radiation at the photon energies h nu=220, 230, 240, 243, and...
Background: In order to generate hypotheses regarding the mechanisms by which 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) causes toxicity, we analyzed global gene expression changes in developing...
Interactive volume rendering in its standard formulation has become an increasingly important tool in many application domains. In recent years several advanced volumetric illumination techniques...
In this paper we describe a novel approach for applying texture mapping to volumetric data sets. In contrast to previous approaches, the presented technique enables a unified integration of 2D and...
We present an algorithm that enables real-time dynamic shading in direct volume rendering using general lighting, including directional lights, point lights and environment maps. real-time...
In recent years, many volumetric illumination models have been proposed, which have the potential to simulate advanced lighting effects and thus support improved image comprehension. Although...
Medical imaging plays a central role in a vast range of healthcare practices. The usefulness of 3D visualizations has been demonstrated for many types of treatment planning. Nevertheless, full...
The visualization of images with a large dynamic range is a difficult task and this is especially the case for gray-level images. In radiology departments, this will force radiologists to review...
Many necessary and desired improvements in healthcare are dependent on progress in medical imaging. As shown in this paper, the challenges targeted by visual analytics (VA) coincide with main...
We present a novel approach to interactive and concurrent volume visualization of functional Magnetic Resonance Imaging (fMRI). While the patient is in the scanner, data is extracted in real-time...
Statistics obtained from seven different direct numerical simulations (DNSs) pertaining to a canonical turbulent boundary layer (TBL) under zero pressure gradient are compiled and compared. The...