Related papers: Infinite Switch Simulated Tempering in Force (FISS…

Self-triggered control (STC) is a sample-and-hold control method aimed at reducing communications within networked-control systems; however, existing STC mechanisms often maximize how late the next sample is, and as such they do not provide…

We introduce an extension to the Weighted Ensemble (WE) path sampling method to restrict sampling to a one dimensional path through a high dimensional phase space. Our method, which is based on the finite-temperature string method, permits…

Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…

Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…

Thermodynamic bulk measurements of binding reactions critically rely on the validity of the law of mass action and the assumption of a dilute solution. Yet important biological systems such as allosteric ligand-receptor binding,…

Many complex systems occurring in the natural or social sciences or economics are frequently described on a microscopic level, e.g., by lattice- or agent-based models. To analyze the states of such systems and their bifurcation structure on…

The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase…

This article focuses on the globally composite adaptive law-based intelligent finite-/fixed- time (FnT/FxT) tracking control issue for a family of uncertain strict-feedback nonlinear systems. First, intelligent approximators with new…

We consider a variable metric and inexact version of the FISTA-type algorithm considered in (Chambolle, Pock, 2016, Calatroni, Chambolle, 2019) for the minimization of the sum of two (possibly strongly) convex functions. The proposed…

Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…

Cell injection is a technique in the domain of biological cell micro-manipulation for the delivery of small volumes of samples into the suspended or adherent cells. It has been widely applied in various areas, such as gene injection,…

This paper introduces Force Matching (ForM), a novel framework for generative modeling that represents an initial exploration into leveraging special relativistic mechanics to enhance the stability of the sampling process. By incorporating…

A platform trial with a master protocol provides an infrastructure to ethically and efficiently evaluate multiple treatment options in multiple diseases. Given that certain study drugs can enter or exit a platform trial, the randomization…

We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…

This study proposes a simple and practical approach based on in-vitro measurements and in-silico simulation using the likelihood-free Bayesian inference with the finite element method simultaneously for stochastic calibration and…

Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to…

Often, constraints arise in deployment settings where even lightweight parameter updates e.g. parameter-efficient fine-tuning could induce model shift or tuning instability. We study test-time adaptation of foundation models for few-shot…

Smart training set selections procedures enable the reduction of data needs and improves predictive robustness in machine learning problems relevant to chemistry. We introduce Gradient Guided Furthest Point Sampling (GGFPS), a simple…

Thompson sampling (TS) is a Bayesian randomized exploration strategy that samples options (e.g., system parameters or control laws) from the current posterior and then applies the selected option that is optimal for a task, thereby…

Rare events in molecular dynamics are often related to noise-induced transitions between different macroscopic states (e.g., in protein folding). A common feature of these rare transitions is that they happen on timescales that are on…