相关论文: Self-Organized Criticality: A Magic Wand for Prote…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
Self-Organizing Map algorithms have been used for almost 40 years across various application domains such as biology, geology, healthcare, industry and humanities as an interpretable tool to explore, cluster and visualize high-dimensional…
What spatial frequency information do humans and neural networks use to recognize objects? In neuroscience, critical band masking is an established tool that can reveal the frequency-selective filters used for object recognition. Critical…
In this paper, we introduce an approach to the protein folding problem from the point of view of statistical physics. Protein folding is a stochastic process by which a polypeptide folds into its characteristic and functional 3D structure…
Driven soft athermal systems may display a reversible-irreversible transition between an absorbing, arrested state and an active phase where a steady-state dynamics sets in. A paradigmatic example consists in cyclically sheared suspensions…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
In this paper, we formulate the new multi-objective coverage (MOC) problem where our goal is to identify a small set of representative samples whose predicted outcomes broadly cover the feasible multi-objective space. This problem is of…
Cellular manufacturing (CM) is an approach that includes both flexibility of job shops and high production rate of flow lines. Although CM provides many benefits in reducing throughput times, setup times, work-in-process inventories but the…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
Self-Organising Maps (SOM) are Artificial Neural Networks used in Pattern Recognition tasks. Their major advantage over other architectures is human readability of a model. However, they often gain poorer accuracy. Mostly used metric in SOM…
Soft Actor-Critic (SAC) is one of the state-of-the-art off-policy reinforcement learning (RL) algorithms that is within the maximum entropy based RL framework. SAC is demonstrated to perform very well in a list of continous control tasks…
We show that correlated dynamics and long time memory persist in self-organized criticality (SOC) systems even when forced away from the defined critical point that exists at vanishing drive strength. These temporal correlations are found…
As feature sizes shrink to the nanometer scale, accurately transferring circuit patterns from photomasks to silicon wafers becomes increasingly challenging. Optical proximity correction (OPC) is widely used to ensure pattern fidelity and…
Second-order optimization methods offer notable advantages in training deep neural networks by utilizing curvature information to achieve faster convergence. However, traditional second-order techniques are computationally prohibitive,…
We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as…
The hypothesis of self-organized criticality explains the existence of long-range `space-time' correlations, observed inseparably in many natural dynamical systems. A simple link between these correlations is yet unclear, particularly in…
A novel approach to protein multiple sequence alignment is discussed: substantially this method counterparts with substitution matrix based methods (like Blosum or PAM based methods), and implies a more deterministic approach to…
Structural Maintenance of Chromosomes, SMCs, proteins have long rod like structures immersed in water. Here we use our hydroanalytic methods based on amino acid sequences to discuss their dynamics at multiple length scales identified by…