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Implicit solvent models (ISMs) promise to deliver the accuracy of explicit solvent simulations at a fraction of the computational cost. However, despite decades of development, their accuracy has remained insufficient for many critical…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Intergranular fracture in polycrystals is often simulated by finite elements coupled to a cohesive-zone model for the interfaces, requiring cohesive laws for grain boundaries as a function of their geometry. We discuss three challenges in…
In this paper we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
The charged environment within a dense plasma leads to the phenomenon of ionization potential depression (IPD) for ions embedded in the plasma. Accurate predictions of the IPD effect are of crucial importance for modeling atomic processes…
We assess the quantitative accuracy of the particle-in-cell (PIC) approximation used in recent ab initio predictions of the thermodynamic properties of hexagonal-close-packed iron at the conditions of the Earth's inner core. The assessment…
Understanding the microstuctural evolution during the sintering process is of high relevance as it is a key part in many industrial manufacturing processes. Simulations are one avenue to achieve this understanding, especially field-resolved…
Irradiation Assisted Stress Corrosion Cracking (IASCC) is a material degradation phenomenon affecting austenitic stainless steels used in nuclear Pressurized Water Reactors (PWR), leading to the initiation and propagation of intergranular…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly.…
Models for prediction of drag forces within a particle cloud following shock-acceleration are evaluated with the aid of results from particle-resolved simulations in order to quantify how much the disturbances introduced by the proximity of…
High-resolution structural information on membrane proteins is essential for understanding cell biology and for structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide {\AA}ngstrom-level…
Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of…
The assembly of curved protein rods on fluid membranes is studied using implicit-solvent meshless membrane simulations. As the rod curvature increases, the rods on a membrane tube assemble along the azimuthal direction first and…
The construction of accurate interatomic potentials, and related fields of forces, from equilibrium conformational distributions of molecules is a crucial step in coarse-grained modeling. In this work we show that in order to develop…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
The elastic and inelastic proton scattering on $^{18,20,22}$O nuclei are studied in a folding model formalism of nucleon-nucleus optical potential and inelastic form factor. The DDM3Y effective interaction is used and the ground state…
A statistical model of protein families, called profile conditional random fields (CRFs), is proposed. This model may be regarded as an integration of the profile hidden Markov model (HMM) and the Finkelstein-Reva (FR) theory of protein…