While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics. In this chapter we explore basic physical and chemical concepts required to understand protein folding. We introduce major (de)stabilising factors of folded protein structures such as the hydrophobic effect and backbone entropy. In addition, we consider different states along the folding pathway, as well as natively disordered proteins and aggregated protein states. In this chapter, an intuitive understanding is provided about the protein folding process, to prepare for the next chapter on the thermodynamics of protein folding. In particular, it is emphasized that protein folding is a stochastic process and that proteins unfold and refold in a dynamic equilibrium. The effect of temperature on the stability of the folded and unfolded states is also explained.

The prediction of protein stability changes following single-point mutations plays a pivotal role in computational biology, particularly in areas like drug discovery, enzyme reengineering, and genetic disease analysis. Although deep-learning strategies have pushed the field forward, their use in standard workflows remains limited due to resource demands. Conversely, potential-like methods are fast, intuitive, and efficient. Yet, these typically estimate Gibbs free energy shifts without considering the free-energy variations in the unfolded protein state, an omission that may breach mass balance and diminish accuracy. This study shows that incorporating a mass-balance correction (MBC) to account for the unfolded state significantly enhances these methods. While many machine learning models partially model this balance, our analysis suggests that a refined representation of the unfolded state may improve the predictive performance.

Multi-Agent Pathfinding (MAPF) plays a critical role in various domains. Traditional MAPF methods typically assume unit edge costs and single-timestep actions, which limit their applicability to real-world scenarios. MAPFR extends MAPF to handle non-unit costs with real-valued edge costs and continuous-time actions, but its geometric collision model leads to an unbounded state space that compromises solver efficiency. In this paper, we propose MAPFZ, a novel MAPF variant on graphs with non-unit integer costs that preserves a finite state space while offering improved realism over classical MAPF. To solve MAPFZ efficiently, we develop CBS-NIC, an enhanced Conflict-Based Search framework incorporating time-interval-based conflict detection and an improved Safe Interval Path Planning (SIPP) algorithm. Additionally, we propose Bayesian Optimization for Graph Design (BOGD), a discretization method for non-unit edge costs that balances efficiency and accuracy with a sub-linear regret bound. Extensive experiments demonstrate that our approach outperforms state-of-the-art methods in runtime and success rate across diverse benchmark scenarios.

Higher-order spacing statistics in the $m$ superposed spectra of circular random matrices of the same class are studied numerically. We conjecture that for given $m$ (or order $k$) and $β$, the sequence of modified Dyson index $β'(k)$ (or $β'(m)$) obtained using the sum of absolute differences between the cumulative distribution functions method (denoted as $D(β')$) is unique. Also, for a given $k$, the distribution tends to the corresponding $k$-th order Poisson statistics in the limit $m\rightarrow \infty$. The quantum chaotic kicked top model for various Hilbert space dimensions is studied, and it is found to satisfy our conjecture. This involves the numerical verification of $m=2$ case of COE results. Our result can be used as a tool for the characterization of a system and to determine the symmetry structure of the system without desymmetrization of the spectra. Additionally, the comparative study of the higher-order spacing and ratio distributions in both $m=1$ and $m=2$ cases of COE as well as GOE is performed within and across these ensembles numerically using the $D(β')$ method. This study is carried out both by varying the dimension and keeping the number of realizations constant, and vice-versa. The same asymptotic higher-order statistics are observed across COE and GOE in terms of a given spectral fluctuation measure. But, within a given ensemble of COE or GOE, the results of higher-order spacing and ratio distributions agree with each other only up to some lower $k$, and beyond that, they start deviating from each other. Further, the spectral fluctuations of the intermediate map of various dimensions are studied. Various important observations and discussions from the analysis of our extensive numerical computations are presented.

Researchers working in lattice field theory constitute an established community since the early 1990s, and around the same time the online open-access e-print repository arXiv was created. The fact that this field has a specific arXiv section, hep-lat, which is comprehensively used, provides a unique opportunity for a statistical study of its evolution over the last three decades. We present data for the number of entries, $E$, published papers, $P$, and citations, $C$, in total and separated by nations. We compare them to six other arXiv sections (hep-ph, hep-th, gr-qc, nucl-th, quant-ph, cond-mat) and to two socio-economic indices of the nations involved: the Gross Domestic Product (GDP) and the Education Index (EI). We present rankings, which are based either on the Hirsch Index H, or on the linear combination $Σ= E + P + 0.05 C$. We consider both extensive and intensive national statistics, i.e. absolute and relative to the population or to the GDP.

In this paper, we propose, discuss, and validate an online Nonlinear Model Predictive Control (NMPC) method for multi-rotor aerial systems with arbitrarily positioned and oriented rotors which simultaneously addresses the local reference trajectory planning and tracking problems. This work brings into question some common modeling and control design choices that are typically adopted to guarantee robustness and reliability but which may severely limit the attainable performance. Unlike most of state of the art works, the proposed method takes advantages of a unified nonlinear model which aims to describe the whole robot dynamics by explicitly including a realistic physical description of the actuator dynamics and limitations. As a matter of fact, our solution does not resort to common simplifications such as: 1) linear model approximation, 2) cascaded control paradigm used to decouple the translational and the rotational dynamics of the rigid body, 3) use of low-level reactive trackers for the stabilization of the internal loop, and 4) unconstrained optimization resolution or use of fictitious constraints. More in detail, we consider as control inputs the derivatives of the propeller forces and propose a novel method to suitably identify the actuator limitations by leveraging experimental data. Differently from previous approaches, the constraints of the optimization problem are defined only by the real physics of the actuators, avoiding conservative -- and often not physical -- input/state saturations which are present, e.g., in cascaded approaches. The control algorithm is implemented using a state-of-the-art Real Time Iteration (RTI) scheme with partial sensitivity update method. CONTINUES...

The field of information science has greatly developed, and applications in various fields have emerged. In this paper, we evaluated the coding system in the theory of Tsallis entropy for transmission of messages and aimed to formulate the channel capacity by maximization of the Tsallis entropy within a given condition of code length. As a result, we obtained a simple relational expression between code length and code appearance probability and, additionally, a generalized formula of the channel capacity on the basis of Tsallis entropy statistics. This theoretical framework may contribute to data processing techniques and other applications.

We introduce an heterogeneous nonlinear $q$-voter model with zealots and two types of susceptible voters, and study its non-equilibrium properties when the population is finite and well mixed. In this two-opinion model, each individual supports one of two parties and is either a zealot or a susceptible voter of type $q_1$ or $q_2$. While here zealots never change their opinion, a $q_i$-susceptible voter ($i=1,2$) consults a group of $q_i$ neighbors at each time step, and adopts their opinion if all group members agree. We show that this model violates the detailed balance whenever $q_1 \neq q_2$ and has surprisingly rich properties. Here, we focus on the characterization of the model's non-equilibrium stationary state (NESS) in terms of its probability distribution and currents in the distinct regimes of low and high density of zealotry. We unveil the NESS properties in each of these phases by computing the opinion distribution and the circulation of probability currents, as well as the two-point correlation functions at unequal times (formally related to a "probability angular momentum"). Our analytical calculations obtained in the realm of a linear Gaussian approximation are compared with numerical results.

The presence of a large number of infected individuals with few or no symptoms is an important epidemiological difficulty and the main mathematical feature of COVID-19. The A-SIR model, i.e. a SIR (Susceptible-Infected-Removed) model with a compartment for infected individuals with no symptoms or few symptoms was proposed by Giuseppe Gaeta, arXiv:2003.08720 [q-bio.PE] (2020). In this paper we investigate a slightly generalized version of the same model and propose a scheme for fitting the parameters of the model to real data using the time series only of the deceased individuals. The scheme is applied to the concrete cases of Lombardy, Italy and São Paulo state, Brazil, showing different aspects of the epidemics. For each case we show that we may have good fits to the data up to the present, but with very large differences in the future behavior. The reasons behind such disparate outcomes are the uncertainty on the value of a key parameter, the probability that an infected individual is fully symptomatic, and on the intensity of the social distancing measures adopted. This conclusion enforces the necessity of trying to determine the real number of infected individuals in a population, symptomatic or asymptomatic.

Recent calculations further supports the premise that large-scale synchronous firings of neurons may affect molecular processes. The context is scalp electroencephalography (EEG) during short-term memory (STM) tasks. The mechanism considered is $\mathbfΠ = \mathbf{p} + q \mathbf{A}$ (SI units) coupling, where $\mathbf{p}$ is the momenta of free $\mathrm{Ca}^{2+}$ waves $q$ the charge of $\mathrm{Ca}^{2+}$ in units of the electron charge, and $\mathbf{A}$ the magnetic vector potential of current $\mathbf{I}$ from neuronal minicolumnar firings considered as wires, giving rise to EEG. Data has processed using multiple graphs to identify sections of data to which spline-Laplacian transformations are applied, to fit the statistical mechanics of neocortical interactions (SMNI) model to EEG data, sensitive to synaptic interactions subject to modification by $\mathrm{Ca}^{2+}$ waves.