Related papers: A Continuum Poisson-Boltzmann Model for Membrane C…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Water plays a fundamental role in the structure and function of proteins and other biomolecules. The thermodynamic profile of water molecules surrounding a protein are critical for ligand binding and recognition. Therefore, identifying the…
We model filtration of a feed solution, containing both small and large foulant particles, by a membrane filter. The membrane interior is modeled as a network of pores, allowing for the simultaneous adsorption of small particles and sieving…
The ensemble average of physical properties of molecules is closely related to the distribution of molecular conformations, and sampling such distributions is a fundamental challenge in physics and chemistry. Traditional methods like…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
The prediction of pressure and flow distributions inside porous membranes is important if the geometry deviates from single-bore tubular geometries. This task remains challenging, especially when considering local porosity variations caused…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
We map molecular dynamics simulations of fluid-fluid interfaces onto mesoscale continuum theories for partially miscible fluids. Unlike most previous work, we examine not only the interface order parameter and density profiles, but also the…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Markov state models (MSMs) have been successful in computing metastable states, slow relaxation timescales and associated structural changes, and stationary or kinetic experimental observables of complex molecules from large amounts of…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
Simulation of fluid flow in porous media has many applications, from the micro-scale (cell membranes, filters, rocks) to macro-scale (groundwater, hydrocarbon reservoirs, and geothermal) and beyond. Direct simulation of flow in porous media…
Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K+ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to…
Multi-component fluid flow simulations in multi-scale porous structures often involve regions that are under-resolved at practical computational resolutions. Accurately capturing the contributions from these unresolved regions is critical.…
The Poisson-Boltzmann (PB) model is a widely used implicit solvent model in protein simulations. Although variants, such as the size modified PB and nonlocal modified PB models, have been developed to account for ionic size effects and…
Identifying the entire set of complexes is essential not only to understand complex formations, but also to map the high level organisation of the cell. Computational prediction of protein complexes faces several challenges including the…
Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins…
Present work attempts to identify the roles of flow- and geometric-variables on the scaling factor which is a necessary parameter for modeling the apparent viscosity of non-Newtonian fluid in porous media. While idealizing the porous media…