相关论文: Plumbing Analog of Molecular Computation
Routinely navigating through an ever-changing and unsteady environment, and utilizing chemical energy, molecular motors transport the cell's crucial components, such as neurotransmitters and organelles. They generate force and pull cargo,…
The asymmetric Hopfield model is used to simulate signaling dynamics in gene/transcription factor networks. The model allows for a direct mapping of a gene expression pattern into attractor states. We analyze different control strategies…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
Molecular fluids show rich and complicated dynamics close to the glass transition. Some of these observations are related to the fact that translational and orientational degrees of freedom couple in nontrivial ways. A model system which…
Key features of biological activity can often be captured by transitions between a finite number of semi-stable states that correspond to behaviors or decisions. We present here a broad class of dynamical systems that are ideal for modeling…
Water molecules inside G-protein coupled receptor have recently been spotlighted in a series of crystal structures. To decipher the dynamics and functional roles of internal waters in GPCR activity, we studied A$_{\text{2A}}$ adenosine…
Specific molecular interactions underlie unexpected and useful phenomena in nanofluidic systems, but require descriptions that go beyond traditional macroscopic hydrodynamics. In this letter, we demonstrate how equilibrium molecular…
We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is…
The paper presents a two-phase hydrodynamic model for the numerical simulation of collective motion in a thin layer of active colloids containing spherical microswimmers. The model accounts for three fundamental mechanisms governing the…
Crystal nucleation is relevant across the domains of fundamental and applied sciences. However, in many cases its mechanism remains unclear due to a lack of temporal or spatial resolution. To gain insights to the molecular details of…
Water management is one of the most critical aspects of our society, together with population increase and climate change. Water scarcity requires a better characterization and monitoring of Water Distribution Networks (WDNs). This paper…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Bioprocess mechanistic modeling is essential for advancing intelligent digital twin representation of biomanufacturing, yet challenges persist due to complex intracellular regulation, stochastic system behavior, and limited experimental…
Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
We present the multicomponent functionalized free energies that characterize the low-energy packings of amphiphilic molecules within a membrane through a correspondence to connecting orbits within a reduced dynamical system. To each…
The macroscopic behaviour of active matter arises from nonequilibrium microscopic processes. In soft materials, active stresses typically drive macroscopic shape changes, which in turn alter the geometry constraining the microscopic…
The high-pressure transportation process of pipeline necessitates an accurate hydraulic transient simulation tool to prevent slack line flow and over-pressure, which can endanger pipeline operations. However, current numerical solution…
In active transport molecular communication (ATMC), information particles are actively transported from a transmitter to a receiver using special proteins. Prior work has demonstrated that ATMC can be an attractive and viable solution for…