Molecular dynamics with constrained nuclear electronic orbital density functional theory: Accurate vibrational spectra from efficient incorporation of nuclear quantum effects

Nuclear quantum effects play a crucial role in many chemical and biological systems involving hydrogen atoms yet are difficult to include in practical molecular simulations. In this Letter, we combine our recently developed methods of constrained nuclear-electronic orbital density functional theory (cNEO-DFT) and constrained minimized energy surface molecular dynamics (CMES-MD) to create a new method for accurately and efficiently describing nuclear quantum effects in molecular simulations. Using this new method, dubbed cNEO-MD, the vibrational spectra of a set of small molecules are calculated and compared with those from conventional ab initio molecular dynamics (AIMD) as well as from experiments. With the same formal scaling, cNEO-MD greatly outperforms AIMD in describing the vibrational modes with significant hydrogen motion characters, demonstrating the promise of cNEO-MD for simulating chemical and biological systems with significant nuclear quantum effects.

Infusing Autopoietic and Cognitive Behaviors into Digital Automata to Improve their Sentience, Resilience and Intelligence

The holy grail of Artificial Intelligence (AI) has been to mimic human intelligence using computing machines. Autopoiesis which refers to a system with well-defined identity and is capable of re-producing and maintaining itself and cognition which is the ability to process information, apply knowledge, and change the circumstance are associated with resilience and intelligence. While classical computer science (CCS) with symbolic and sub-symbolic computing has given us tools to decipher the mysteries of physical, chemical and biological systems in nature and allowed us to model, analyze various observations and use information to optimize our interactions with each other and with our environment, it falls short in reproducing even the basic behaviors of living organisms. We present the foundational shortcomings of CCS and discuss the science of infor-mation processing structures (SIPS) that allows us to fill the gaps. SIPS allows us to model su-per-symbolic computations and infuse autopoietic and cognitive behaviors into digital machines. They use common knowledge representation from the information gained using both symbolic and sub-symbolic computations in the form of system-wide knowledge networks consisting of knowledge nodes and information sharing channels with other knowledge nodes. The knowledge nodes wired together fire together to exhibit autopoietic and cognitive behaviors.

Gaussian Distribution Model for Detecting Dangerous Operating Conditions in Industrial Fish Farming

The development of better monitoring technologies, the early combat of outbreaks, massive mortality, and promoting sustainability are challenges that the aquaculture industry still faces, and the development of solutions for this is an open problem. In this paper, focusing our attention on monitoring technologies as a promising solution to these issues, we report a Gaussian distribution model for detecting dangerous operating conditions in industrial fish farming. This approach allows us to indicate through a 2D image visualization when fish production is under normal, warning, or dangerous operating conditions. Furthermore, our proposed method has promising possibilities for application in the most varied fields of science, given that the mathematical procedure described allows us to discover the fundamental statistical structure of physical, chemical, and biological systems governed by laws of a probabilistic nature.

Biomimetics Integrated Nanoscience in Dental Tissue Regeneration : A Review

At a fundamental level, nanotechnology helps to manipulate individual atoms and molecules to produce novel structures with unique properties or improved properties. It involves the production. and applications of physical, chemical, and biological systems and materials at a size scale ranging 1-100 nm. Even though nanotechnology was first introduced over half a century ago, its progress has been slow, but in the last decade, nanotechnology has caught the imagination of scientists and the general public. Nanotechnology offers us the ability to design materials with totally new desirable characteristics Nanotechnology can be approached in two ways: "top-down" and "bottom-up" approaches .Nature uses the bottom-up approach and builds diverse structures in biological systems. The complexity and functionality of these structures is truly amazing. If we can control in fine detail the way in which these structures can be produced in the same way as nature does, remarkable and rapid advances can be made in the field of medicine and dentistry. Nanomaterials will be used far more widely and will yield superior properties and when com bined with biotechnology, laser and digital guided surgery will thus provide excellent dental care. Biomimetics and nanotechnology have given us the knowledge to bioengineer lost tooth and regenerate dental structures. In this review article, recent progress in field of nanotechnology integrated dental tissue regeneration and their potential clinical uses are described.

Symmetry breaking meets multisite modification

Multisite modification is a basic way of conferring functionality to proteins, and a key component of post-translational modification networks. Additional interest in multisite modification stems from its capability of acting as complex information processors. In this paper we connect two seemingly disparate themes: symmetry and multisite modification. We examine different classes of random modification networks of substrates involving separate or common enzymes. We demonstrate that under different instances of symmetry of the modification network (invoked explicitly or implicitly and discussed in the literature), the biochemistry of multisite modification can lead to the symmetry being broken. This is shown computationally and consolidated analytically, revealing parameter regions where this can (and in fact does) happen, and characteristics of the symmetry broken state. We discuss the relevance of these results in situations where exact symmetry is not present. Overall, through our study we show how symmetry breaking (i) can confer new capabilities to protein networks, including concentration robustness of different combinations of species (in conjunction with multiple steady states) (ii) could have been the basis for ordering of multisite modification, which is widely observed in cells (iii) can significantly impact information processing in multisite modification and in cell signalling networks/pathways where multisite modification is present (iv) can be a fruitful new angle for engineering in synthetic biology and chemistry. All in all, the emerging conceptual synthesis provides a new vantage point for the elucidation and the engineering of molecular systems at the junction of chemical and biological systems.

Cluster Morphology of Colloidal Systems With Competing Interactions

Reversible aggregation of purely short-ranged attractive colloidal particles leads to the formation of clusters with a fractal dimension that only depends on the second virial coefficient. The addition of a long-ranged repulsion to the potential modifies the way in which the particles aggregate into clusters and form intermediate range order structures, and have a strong influence on the dynamical and rheological properties of colloidal dispersions. The understanding of the effect of a long-ranged repulsive potential on the aggregation mechanisms is scientifically and technologically important for a large variety of physical, chemical and biological systems, including concentrated protein solutions. In this work, the equilibrium cluster morphology of particles interacting through a short-ranged attraction plus a long-ranged repulsion is extensively studied by means of Monte Carlo computer simulations. Our findings point out that the addition of the repulsion affects the resulting cluster morphology and allows one to have a full control on the compactness or fractal dimension of the aggregates at a given thermodynamic condition. This allows us to manipulate the reversible aggregation process and, therefore, to finely tune the resulting building blocks of materials at large length scales.

Boosting Performance by Water Solvation Shell with Hydrogen Bonds on Protonic Ionic Liquid: Insights into the Acid Catalysis of Glycosidic Bond

Hydrogen-bonding (HB) induced by water solvation shell is vital in the chemical and biological systems. Herein, HBs related to the binding behavior of protonic ionic liquids (PIL) with water molecules...

Glycosyl disulfides: importance, synthesis and application to chemical and biological systems

This review explores methodologies for the preparation of glycosyl disulfides, their utility as intermediates in carbohydrate synthesis, and evaluates their biological impact in glycoscience and beyond.