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Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors.…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this…
Mathematical models of stem cell differentiation are commonly based upon the concept of subsequent cell fate decisions, each controlled by a gene regulatory network. These networks exhibit a multistable behavior and cause the system to…
An activated process consists of energy activation and barrier crossing; the former is a prerequisite for the latter. Barrier crossing has been studied extensively, but energy activation has been overlooked due to a lack of means to gauge…
Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins…
We present a microscopic approach to quantum dissipation and sketch the derivation of the kinetic equation describing the evolution of a simple quantum system in interaction with a complex quantum system. A typical quantum complex system is…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
In this paper, we propose a method to build molecular cages designed to capture a specific substrate. We model a cage as a graph of atoms with coordinates in space, and several constraints on their edges (degree, length and angle). We use a…
Neural network (NN) interatomic potentials provide fast prediction of potential energy surfaces, closely matching the accuracy of the electronic structure methods used to produce the training data. However, NN predictions are only reliable…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Using control barrier functions (CBFs) as safety filters provides a computationally inexpensive yet effective method for constructing controllers in safety-critical applications. However, using CBFs requires the construction of a valid CBF,…
The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular…
A new upscaling procedure that provides 1D representations of 2D mixing-limited reactive transport systems is developed and applied. A key complication with upscaled models in this setting is that the procedure must differentiate between…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…
Catalyst design is crucial for materials synthesis, especially for complex reaction networks. Strategies like collaborative catalytic systems and multifunctional catalysts are effective but face challenges at the nanoscale. Carbon nanotube…
The paper establishes a methodology to overcome the difficulty of dynamic frame alignment and system separation in impedance modeling of ac grids, and thereby enables impedance-based whole-system modeling of generator-converter composite…
Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…
Integrating uncertainties in the design process of reinforced concrete rail bridges, in a fully probabilistic framework, makes their design more complex and challenging. To propagate these uncertainties and convey their influence on the…