Related papers: Testing a New Monte Carlo Strategy for Folding Mod…
The conformational properties of flexible polymers in d dimensions in environments with extended defects are analyzed both analytically and numerically. We consider the case, when structural defects are correlated in \varepsilon_d…
The widely used double-bridging hybrid (DBH) method for equilibrating simulated entangled polymer melts [R. Auhl et al., J. Chem. Phys. v. 119, p. 12718, 2003] loses its effectiveness as chain stiffness increases into the semiflexible…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
At the scale of the individual cell, protein production is a stochastic process with multiple time scales, combining quick and slow random steps with discontinuous and smooth variation. Hybrid stochastic processes, in particular…
We introduce eigenpruning, a method that removes singular values from weight matrices in an LLM to improve its performance in a particular task. This method is inspired by interpretability methods designed to automatically find subnetworks…
Advanced algorithms are necessary to obtain faster-than-real-time dynamic simulations in a number of different physical problems that are characterized by widely disparate time scales. Recent advanced dynamic Monte Carlo algorithms that…
Due to their substantial sizes, large language models (LLMs) are typically deployed within a single-backbone multi-tenant framework. In this setup, a single instance of an LLM backbone must cater to multiple users or tasks through the…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
We determined scaling laws for the numerical effort to find the optimal configurations of a simple model potential energy surface (PES) with a perfect funnel structure that reflects key characteristics of the protein interactions.…
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…
The preferential sampling of locations chosen to observe a spatio-temporal process has been identified as a major problem across multiple fields. Predictions of the process can be severely biased when standard statistical methodologies are…
In low-temperature high-density plasmas quantum effects of the electrons are becoming increasingly important. This requires the development of new theoretical and computational tools. Quantum Monte Carlo methods are among the most…
Multivariate probit models (MPM) have the appealing feature of capturing some of the dependence structure between the components of multidimensional binary responses. The key for the dependence modelling is the covariance matrix of an…
Several strategies have been recently proposed in order to improve Monte Carlo sampling efficiency using machine learning tools. Here, we challenge these methods by considering a class of problems that are known to be exponentially hard to…
We study the peculiarities of stretching of globular polymer macromolecules in a disordered (crowded) environment, using the model of self-attracting self-avoiding walks on site-diluted percolative lattices in space dimensions d=3. Applying…
Reparameterized diffusion models (RDMs) have recently matched autoregressive methods in protein generation, motivating their use for challenging tasks such as designing membrane proteins, which possess interleaved soluble and transmembrane…
Lattice models have been used extensively over the past thirty years to examine the principles of protein folding and design. These models can be used to determine the conformation of the lowest energy fold out of a large number of possible…