Related papers: A Coarse-Grained Lattice Model for Molecular Recog…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Molecule representation learning is crucial for understanding and predicting molecular properties. However, conventional atom-centric models, which treat chemical bonds merely as pairwise interactions, often overlook complex bond-level…
A Restricted Boltzmann Machine (RBM) is an unsupervised machine-learning bipartite graphical model that jointly learns a probability distribution over data and extracts their relevant statistical features. As such, RBM were recently…
Complex colloidal fluids, such as emulsions stabilized by complex shaped particles, play an important role in many industrial applications. However, understanding their physics requires a study at sufficiently large length scales while…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
In this work we propose a hierarchy of Monte Carlo methods for sampling equilibrium properties of stochastic lattice systems with competing short and long range interactions. Each Monte Carlo step is composed by two or more sub - steps…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…
A simple d-dimensional lattice model is proposed, incorporating some degree of frustration and thus capable of describing some aspects of molecular orientation in covalently bound molecular solids. For d=2 the model is shown to be…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
Phage lambda is one of the most studied biological models in modern molecular biology. Over the past 50 years quantitative experimental knowledge on this biological model has been accumulated at all levels: physics, chemistry, genomics,…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, $Omega_{c}$, is introduced to quantitatively assess the degree of cooperativity in lattice models and in real…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
We investigate and provide optimal sets of reaction coordinates for mixed pairs of molecules displaying polar, uniaxial, or spherical symmetry in two and three dimensions. These coordinates are non-redundant, i.e., they implicitly involve…