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Recent advances in artificial intelligence have propelled the development of innovative computational materials modeling and design techniques. Generative deep learning models have been used for molecular representation, discovery, and…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…
Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
Waste production, carbon dioxide atmospheric accumulation, and dependence on finite natural resources are expressions of the unsustainability of the current industrial networks that supply fuels, energy, and manufacturing products. In…
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments we envisaged how kinesin, a…
Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…
A challenging problem when studying a dynamical system is to find the interdependencies among its individual components. Several algorithms have been proposed to detect directed dynamical influences between time series. Two of the most used…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
This work is concerned with synthesizing safety controllers for discrete-time nonlinear systems beyond polynomials with unknown mathematical models using the notion of k-inductive control barrier certificates (k-CBCs). Conventional CBC…
Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze…
We examined theory for force-induced unbinding on a two-dimensional free energy surface where the internal dynamics of biomolecules is coupled with the rupture process under constant tension f. We show that only if the transition state…
Designing reaction pathways that maximize the production of a target compound in a given metabolic network is a fundamental problem in systems biology. In this study, we systematically explore the non-oxidative glycolysis metabolic network,…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's…
The design of desired behaviors in mechanical metamaterials has produced remarkable advances but has generally neglected two aspects - the inevitable presence of undesired behaviors and the role of dynamics in avoiding such behaviors.…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…