相关论文: Dominant Folding Pathways of a WW Domain

The accurate simulation of complex biochemical phenomena has historically been hampered by the computational requirements of high-fidelity molecular-modeling techniques. Quantum mechanical methods, such as ab initio wave-function (WF)…

We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…

We undertake a quantitative comparison of multi-fragmentation reactions, as modeled by two different approaches: the Antisymmetrized Molecular Dynamics (AMD) and the momentum-dependent stochastic mean-field (SMF) model. Fragment observables…

We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three…

A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…

The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…

How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…

We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…

Differential-driven wheeled robots (DWR) represent the quintessential type of mobile robots and find extensive appli- cations across the robotic field. Most high-performance control approaches for DWR explicitly utilize the linear and…

We study the electric properties of single-stranded DNA molecules with hairpin-like shapes in the presence of a magnetic flux. It is shown that the current amplitude can be modulated by the applied field. The details of the electric…

We present molecular dynamics (MD) results to discuss wetting kinetics in binary fluid mixtures ($A:B=50:50$) undergoing surface-directed spinodal decomposition (SDSD) on an amorphous wall. Our simulations show the formation of a wetting…

An in-domain finite dimensional controller for a class of distributed parameter systems on a one-dimensional spatial domain formulated under the port-Hamiltonian framework is presented. Based on [25] where positive feedback and a late…

We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…

The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…

In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…

In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…

Studying the pathways of ligand-receptor binding is essential to understand the mechanism of target recognition by small molecules. The binding free energy and kinetics of protein-ligand complexes can be computed using molecular dynamics…

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…

We investigate the domain structure of pair contact process with diffusion (PCPD). PCPD is a stochastic reaction-diffusion model which evolves by the competition of two binary reactions, $2A \to 3A$ and $2A \to 0$. In addition, each…

Drifting pattern domains (DPDs), moving localized patches of traveling waves embedded in a stationary (Turing) pattern background and vice versa, are observed in simulations of a reaction-diffusion model with nonlocal coupling. Within this…