相关论文: Current MD forcefields fail to capture key feature…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different…
We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The…
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
Dense granular clusters often behave like macro-particles. We address this interesting phenomenon in a model system of inelastically colliding hard disks inside a circular box, driven by a thermal wall at zero gravity. Molecular dynamics…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein-protein interactions. However, many commonly used methods to predict these effects perform poorly in important…
Membrane curvature sensing is essential for a diverse range of biological processes. Recent experiments have revealed that a single nanometer-sized septin protein can distinguish between membrane-coated glass beads of one micron and three…
Intrinsically disordered proteins (IDPs) play a significant role in intracellular phenomena and are known to exist in an ensemble of inter-converting conformations in solution. Accurately modeling the conformations of IDPs in solution poses…
Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
Once the magnesium alloy was implanted in the body, it was immediately covered with plasma proteins. The coated alloy surface promoted the adsorption and growth of osteoblasts. Herein, in vitro biological reactions of the ZK60 and AZ31…
Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
We use machine learning to enable large-scale molecular dynamics (MD) of a correlated electron model under the Gutzwiller approximation scheme. This model exhibits a Mott transition as a function of on-site Coulomb repulsion $U$. The…