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The endoplasmic reticulum (ER) is a network of sheet-like and tubular structures that spans much of a cell and contains molecules undergoing diffusive searches for targets, such as unfolded proteins searching for chaperones and…

Modeling the dynamical flows on networks of biomolecular machines often entails computing node populations and edge fluxes with Master Equations and correlating machine performance with entropy production. But this alone is not sufficient…

Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…

Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function.…

Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…

Cell type-specific gene expression patterns are represented as memory states of a Hopfield neural network model. It is shown that order parameters of this model can be interpreted as concentrations of master transcription regulators that…

Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computational costs and energy-barrier trapping. This paper presents…

The design of biological systems is hindered by uncertainty arising from both intrinsic stochasticity of biomolecular reactions and variability across laboratory or experimental conditions. In this work, we present a sequential framework to…

Cells contain elaborate and interconnected networks of protein polymers which make up the cytoskeleton. The cytoskeleton governs the internal positioning and movement of vesicles and organelles, and controls dynamic changes in cell…

New approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, enforced by new crossover operators, especially worked out for…

The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…

The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…

Molecule synthesis through machine learning is one of the fundamental problems in drug discovery. Current data-driven strategies employ one-step retrosynthesis models and search algorithms to predict synthetic routes in a top-bottom manner.…

Templated copying is the central operation by which biology produces complex molecules. Cells copy sequence information from DNA to RNA and on into proteins, which are the molecules responsible for the function and regulation of cellular…

We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…

Path following controllers make the output of a control system approach and traverse a pre-specified path with no apriori time parametrization. In this paper we present a method for path following control design applicable to framed curves…

Drug optimization has become increasingly crucial in light of fast-mutating virus strains and drug-resistant cancer cells. Nevertheless, it remains challenging as it necessitates retaining the beneficial properties of the original drug…

Accurate tracking of planned trajectories in the presence of perturbations is an important problem in control and robotics. Symmetry is a fundamental mathematical feature of many dynamical systems and exploiting this property offers the…

Due to the vast design space of molecules, generating molecules conditioned on a specific sub-structure relevant to a particular function or therapeutic target is a crucial task in computer-aided drug design. Existing works mainly focus on…

This paper introduces a framework to systematically optimize the control and design of an electric vehicle transmission, connecting powertrain sizing studies to detailed gearbox design methods. To this end, we first create analytical models…