相关论文: Plumbing Analog of Molecular Computation
Energy-based modelling brings engineering insight to the understanding of biomolecular systems. It is shown how well-established control engineering concepts, such as loop-gain, arise from energy feedback loops and are therefore amenable to…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
Geometric, topological and graph theory modeling and analysis of biomolecules are of essential importance in the conceptualization of molecular structure, function, dynamics, and transport. On the one hand, geometric modeling provides…
Discriminating between correct and incorrect substrates is a core process in biology but how is energy apportioned between the conflicting demands of accuracy ($\mu$), speed ($\sigma$) and total entropy production rate ($P$)? Previous…
A qualitative model is presented, suggesting gravitational information is transduced into biological systems primarily by its effect on spatially organised membrane and cytoplasmic flows. Continuous low affinity interactions between…
Allosteric signaling in biological molecules, which may be viewed as specific action at a distance due to localized perturbation upon binding of ligands or changes in environmental cues, is pervasive in biology. Phenomenological MWC and KNF…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Arterial blood pressure is a key vital sign for the health of the human body. As such, accurate and reproducible measurement techniques are necessary for successful diagnosis. Blood pressure measurement is an example of molecular…
In the quest for highest performance in scientific computing, we present a novel framework that relies on high-bandwidth communication between GPUs in a compute cluster. The framework offers linear scaling of performance for explicit…
Standard Spiking Neural Network (SNN) models typically neglect metabolic constraints, treating neurons as energetically unconstrained components. We bridge this gap by implementing a conductance-based leaky integrate-and-fire (gLIF)…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
G-protein coupled receptors (GPCRs), a major gatekeeper of extracellular signals on plasma membrane, are unarguably one of the most important therapeutic targets. Given the recent discoveries of allosteric modulations, an allosteric wiring…
Reservoir computing has been shown to be a useful framework for predicting critical transitions of a dynamical system if the bifurcation parameter is also provided as an input. Its utility is significant because in real-world scenarios, the…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
The origin of allometric scaling patterns that are multiples of 1/4 has long fascinated biologists. While not universal, scaling relationships with exponents that are close to multiples of 1/4 are common and have been described in all major…
A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be…
Non-equilibrium molecular-scale dynamics, where fast electron transport couples with slow chemical state evolution, underpins the complex behaviors of molecular memristors, yet a general model linking these dynamics to neuromorphic…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…