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The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
In this paper, we propose a data-driven economic model predictive control (EMPC) scheme with generalized terminal constraint to control an unknown linear time-invariant system. Our scheme is based on the Fundamental Lemma to predict future…
The invention of CPU-centric computing paradigm was incredible breakthrough of computer science that revolutionized our everyday life dramatically. However, the CPU- centric paradigm is based on the Turing machine concept and, as a result,…
Energy-Based Models (EBMs) have been widely used for generative modeling. Contrastive Divergence (CD), a prevailing training objective for EBMs, requires sampling from the EBM with Markov Chain Monte Carlo methods (MCMCs), which leads to an…
In most of the cases, the experimental study of Nanotechnology involves high cost for Laboratory set-up and the experimentation processes were also slow. So, one cannot rely on experimental nanotechnology alone. As such, the Computer-Based…
A notion of entropy is introduced for causal fermion systems. This entropy is a measure of the state of disorder of a causal fermion system at a given time compared to the vacuum. The definition is given both in the finite and…
Entropy serves as a central observable in equilibrium thermodynamics. However, many biological and ecological systems operate far from thermal equilibrium. Here we show that entropy production can characterize the behavior of such…
For decades, computational chemistry has been posited as one of the areas in which quantum computing would revolutionize. However, the algorithmic advantages that fault-tolerant quantum computers have for chemistry can be overwhelmed by…
In the last few decades, some hypotheses for entropy production (EP) principles have been forwarded as possible candidates for organizational principles in non-linear non- equilibrium systems. Two important hypotheses will be studied: the…
Free energy calculations are at the heart of physics-based analyses of biochemical processes. They allow us to quantify molecular recognition mechanisms, which determine a wide range of biological phenomena from how cells send and receive…
This letter highlights the entropy exchange phenomenon in a coupled binary inter-correlating system following Haldane's non-linear statistical correlation. A unique coupling between a classical and a quantum-like system at the marginal…
We illustrate how computer-aided methods can be used to investigate the fundamental limits of the caching systems, which are significantly different from the conventional analytical approach usually seen in the information theory…
Living systems maintain or increase local order by working against the Second Law of Thermodynamics. Thermodynamic consistency is restored as they dissipate heat, thereby increasing the net entropy of their environment. Recently introduced…
Computational chemistry grew in a new era of "desktop modeling", which coincided with a growing demand for modeling software, especially from the pharmaceutical industry. Parameterization of models in computational chemistry is an arduous…
The extracellular matrix (ECM) is a highly complex structure through which biochemical and mechanical signals are transmitted. In processes of cell migration, the ECM also acts as a scaffold, providing structural support to cells as well as…
Since the turn of the millennium, computational modelling of biological systems has evolved remarkably and sees matured use spanning basic and clinical research. While the topic of the peri-millennial debate about the virtues and…
Brain-body co-evolution enables animals to develop complex behaviors in their environments. Inspired by this biological synergy, embodied co-design (ECD) has emerged as a transformative paradigm for creating intelligent agents-from virtual…
Understanding deaths and life-death boundaries of cells is a fundamental challenge in biological sciences. In this study, we present a theoretical framework for investigating cell death. We conceptualize cell death as a controllability…
Most of the existing classification methods are aimed at minimization of empirical risk (through some simple point-based error measured with loss function) with added regularization. We propose to approach this problem in a more information…
Understanding how biochemical systems settle into stable states, such as how protein concentrations reach equilibrium, is central to explaining cellular behavior and designing synthetic biological circuits. However, existing analytical…