相关论文: Universality of fold-encoded localized vibrations …
As has long been known to computer scientists, the performance of probabilistic algorithms characterized by relatively large runtime fluctuations can be improved by applying a restart, i.e., episodic interruption of a randomized…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
Long wavelength acoustic phonons are normally weakly coupled to other vibrational modes in a crystalline system. This is particularly problematic in molecular dynamics calculations where vibrations at the system size scale are typically…
In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the…
Understanding how the dynamics of neural networks is shaped by the computations they perform is a fundamental question in neuroscience. Recently, the framework of efficient coding proposed a theory of how spiking neural networks can compute…
The emergent spatial patterns generated by growing bacterial colonies have been the focus of intense study in physics during the last twenty years. Both experimental and theoretical investigations have made possible a clear qualitative…
The TIM-barrel fold is one of the most versatile and ubiquitous protein folds in nature, hosting a wide variety of catalytic activities and functions while serving as a model system in protein biochemistry and engineering. This review…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
Determining the 3D structures of biological molecules is a key problem for both biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising technique for structure estimation which relies heavily on computational methods to…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
We show, through a machine learning approach, that the equilibrium distance, harmonic vibrational frequency, and binding energy of diatomic molecules are universally related. In particular, the relationships between spectroscopic constants…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
The dynamical relaxation and scaling properties of three different variants of the contact process in two spatial dimensions are analysed. Dynamical contact processes capture a variety of contagious processes such as the spreading of…
The controlled dissipation of chemical potentials is the fundamental way cells make a living. Enzyme-mediated catalysis allows the various transformations to proceed at biologically relevant rates with remarkable precision and efficiency.…
We present a new, simple, fast algorithm to numerically evolve disks of inelastically colliding particles surrounding a central star. Our algorithm adds negligible computational cost to the fastest existing collisionless N-body codes, and…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
Excitable media are ubiquitous in nature, and in such systems the local excitation tends to self-organize in traveling waves, or in rotating spiral-shaped patterns in two or three spatial dimensions. Examples include waves during a pandemic…
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…
All cells must keep time to consistently perform vital biological functions. To that end, the coupling and interrelatedness of diverse subsecond events in the complex cellular environment, such as protein folding or translation rates,…