相关论文: Predicting the orientation of adsorbed proteins st…

Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…

We apply the recently developed triangular tessellation technique as presented in [J. de Graaf et al., Phys. Rev. E 80, 051405 (2009)] to calculate the free energy associated with the adsorption of anisotropic colloidal particles at a flat…

Tailoring the functional properties of advanced organic/inorganic heterogeonous devices to their intended technological applications requires knowledge and control of the microscopic structure inside the device. Atomistic quantum mechanical…

In this paper, we propose a selective sampling procedure to preferentially evaluate a potential energy surface (PES) in a part of the configuration space governing a physical property of interest. The proposed sampling procedure is based on…

We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the…

Free-energy-based adaptive biasing methods, such as Metadynamics, the Adaptive Biasing Force (ABF) and their variants, are enhanced sampling algorithms widely used in molecular simulations. Although their efficiency has been empirically…

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The…

A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…

Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…

Enhanced sampling and free energy calculation algorithms of the Thermodynamic Integration family (such as the Adaptive Biasing Force method, ABF) are not based on the direct computation of a free energy surface, but rather of its gradient.…

The adsorption of large ions from solution to a charged surface is investigated theoretically. A generalized Poisson--Boltzmann equation, which takes into account the finite size of the ions is presented. We obtain analytical expressions…

The description of the chemical bond between a solid surface and an atom or a molecule is the fundamental basis for understanding a broad range of scientific problems in heterogeneous catalysis, semiconductor device fabrication, and fuel…

To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…

The behavior of a polyelectrolyte adsorbed on a charged surface of high-dielectric constant is studied by both Monte-Carlo simulation and analytical methods. It is found that in a low ionic strength medium, the transition is first-order…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

A model of a finite cylindrical ion channel through a phospholipid membrane of width $L$ separating two electrolyte reservoirs is studied. Analytical solution of the Poisson equation is obtained for an arbitrary distribution of ions inside…

The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is thus an important parameter for many astrochemical studies. This parameter is usually determined with…

The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into…

A new particle-based sampling and approximate inference method, based on electrostatics and Newton mechanics principles, is introduced with theoretical ground, algorithm design and experimental validation. This method simulates an…

Predicting the change in binding free energy ($\Delta \Delta G$) is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarcity of experimental $\Delta \Delta G$ data,…