Costly punishment sustains indirect reciprocity under low defection detectability.

Cooperation is fundamental to human societies, and indirect reciprocity, where individuals cooperate to build a positive reputation for future benefits, plays a key role in promoting it. Previous theoretical and experimental studies have explored both the effectiveness and limitations of costly punishment in sustaining cooperation. While empirical observations show that costly punishment by third parties is common, some theoretical models suggest it may not be effective in the context of indirect reciprocity, raising doubts about its potential to enhance cooperation.

Hotspot analysis of COVID-19 infection in Tokyo based on influx patterns.

We analyse the relationship between population influx and the effective reproduction number in the 23 wards of Tokyo during the COVID-19 pandemic to estimate hotspots of infection. We identify some patterns of population influx via factor analysis and estimate specific areas as infection-related hotspots by focusing on influx patterns that are highly correlated with the effective reproduction number. As a result, several influx patterns are assumed to be directly related to the subsequent spread of the infection.

Structural dynamics of a designed peptide pore under an external electric field.

Membrane potential is essential in biological signaling and homeostasis maintained by voltage-sensitive membrane proteins. Molecular dynamics (MD) simulations incorporating membrane potentials have been extensively used to study the structures and functions of ion channels and protein pores. They can also be beneficial in designing and characterizing artificial ion channels and pores, which will guide further amino acid sequence optimization through comparison between the predicted models and experimental data.

Receptor-independent regulation of Gα13 by alpha-1-antitrypsin C-terminal peptides.

Alpha-1-antitrypsin (AAT), a circulating serine protease inhibitor, is an acute inflammatory response protein with anti-inflammatory functions. The C-terminal peptides of AAT are found in various tissues and have been proposed as putative bioactive peptides with multiple functions, but its mechanism of action remains unclear. We previously reported that a mouse AAT C-terminal peptide of 35 amino acids (mAAT-C) penetrates plasma membrane and associates guanine nucleotide-binding protein subunit alpha 13 (Gα13).

Investigating self-supervised image denoising with denaturation.

Self-supervised learning for image denoising problems in the presence of denaturation for noisy data is a crucial approach in machine learning. However, theoretical understanding of the performance of the approach that uses denatured data is lacking. To provide better understanding of the approach, in this paper, we analyze a self-supervised denoising algorithm that uses denatured data in depth through theoretical analysis and numerical experiments.

Reducing Numerical Precision Requirements in Quantum Chemistry Calculations.

The abundant demand for deep learning compute resources has created a renaissance in low-precision hardware. Going forward, it will be essential for simulation software to run on this new generation of machines without sacrificing scientific fidelity. In this paper, we examine the precision requirements of a representative kernel from quantum chemistry calculations: the calculation of the single-particle density matrix from a given mean-field Hamiltonian (i.

Data Science for Integrated Dynamic Structural Biology-the 21st IUPAB Congress session summary commentary.

The session "Data Science for Integrated Dynamic Structural Biology" was a notable success at the joint congress of the 21st IUPAB and the 62nd BSJ (Biophysics Society of Japan). This session included four invited talks and one contributed talk, which together delved into recent advancements in computational methods integrating physics, experimental data, and bioinformatics to study the structure and dynamic properties of molecular assemblies and their interactions.

Tandem Mass Spectrometry of Perfluorocarboxylate Anions: Fragmentation Induced by Reactive Species Formed From Microwave Excited Hydrogen and Water Plasmas.

Rationale: Polyfluoroalkyl substances (PFAS) like perfluorooctanoic acid have persistent environmental and physiological effects. This study investigates the degradation of CFCO (n = 1-7) with neutral radical fragmentation under oxygen attachment dissociation (OAD). Unique fragments absent from collision-induced dissociation (CID) are observed.

Similarity between oxygen evolution in photosystem II and oxygen reduction in cytochrome c oxidase via proton coupled electron transfers. A unified view of the oxygenic life from four electron oxidation-reduction reactions.

Basic concepts and theoretical foundations of broken symmetry (BS) and post BS methods for strongly correlated electron systems (SCES) such as electron-transfer (ET) diradical, multi-center polyradicals with spin frustration are described systematically to elucidate structures, bonding and reactivity of the high-valent transition metal oxo bonds in metalloenzymes: photosystem II (PSII) and cytochrome c oxidase (CcO). BS hybrid DFT (HDFT) and DLPNO coupled-cluster (CC) SD(T) computations are performed to elucidate electronic and spin states of CaMnO cluster in the key step for oxygen evolution, namely S [S with Mn(IV) = O + Tyr161-O radical] state of PSII and P [Fe(IV) = O + HO-Cu(II) + Tyr161-O radical] step for oxygen reduction in CcO. The cycle of water oxidation catalyzed by the CaMnO cluster in PSII and the cycle of oxygen reduction catalyzed by the Cu-Fe-Fe-Cu cluster in CcO are examined on the theoretical grounds, elucidating similar concerted and/or stepwise proton transfer coupled electron transfer (PT-ET) processes for the four-electron oxidation in PSII and four-electron reduction in CcO.

Indirect reciprocity under opinion synchronization.

Indirect reciprocity is a key explanation for the exceptional magnitude of cooperation among humans. This literature suggests that a large proportion of human cooperation is driven by social norms and individuals' incentives to maintain a good reputation. This intuition has been formalized with two types of models.

Allosteric changes in the conformational landscape of Src kinase upon substrate binding.

Precise regulation of protein kinase activity is crucial in cell functions, and its loss is implicated in various diseases. The kinase activity is regulated by interconverting active and inactive states in the conformational landscape. However, how protein kinases switch conformations in response to different signals such as the binding at distinct sites remains incompletely understood.

Nuclear Quantum Effects Have a Significant Impact on UV/Vis Absorption Spectra of Chromophores in Water.

Despite the broadly acknowledged importance of solvation effects on measured UV/Vis spectra in the context of solvatochromism or chemical reactions in solution, it is still an open challenge to calculate UV/Vis spectra with predictive accuracy. This is particularly true when it comes to the impact of nuclear quantum effects on these experimental observables. In the present work, we calculate the UV/Vis absorption spectrum of indole in aqueous solution with a combination of a correlated wavefunction method for computing electronic excitation energies and enhanced path integral simulations for rigorous sampling of nuclear configurations including the quantum effects in solution.

RadicalPy: A Tool for Spin Dynamics Simulations.

Radical pairs (electron-hole pairs, polaron pairs) are transient reaction intermediates that are found and exploited in all areas of science, from the hard realm of physics in the form of organic semiconductors, spintronics, quantum computing, and solar cells to the soft domain of chemistry and biology under the guise of chemical reactions in solution, biomimetic systems, and quantum biology. Quantitative analysis of radical pair phenomena has historically been successful by a few select groups. With this in mind, we present an intuitive open-source framework in the Python programming language that provides classical, semiclassical, and quantum simulation methodologies.

Valley-Polarized Topological Phases with In-Plane Magnetization.

The coexistence of valley polarization and topology has considerably facilitated the applications of 2D materials toward valleytronics device technology. However, isolated and distinct valleys are required to observe the valley-related quantum phenomenon. Herein, we report a new mechanism to generate in-plane magnetization direction-dependent isolated valley carriers by preserving or breaking the mirror symmetry in a 2D system.

Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis.

Observing a single biomolecule performing its function is fundamental in biophysics as it provides important information for elucidating the mechanism. High-speed atomic force microscopy (HS-AFM) is a unique and powerful technique that allows the observation of biomolecular motion in a near-native environment. However, the spatial resolution of HS-AFM is limited by the physical size of the cantilever tip, which restricts the ability to obtain atomic details of molecules.

ResiDEM: Analytical Tool for Isomorphous Difference Electron Density Maps Utilizing Dynamic Residue Identification via Density Clustering.

Time-resolved serial femtosecond crystallography (TR-SFX) of biological molecules captures the time-evolved dynamics of the residual motions across crystal structures, enabling the visualization of structural changes in response to chemical and physical stimuli to elucidate the relationship between the structure and function of the system under study. However, interpretations of residual motions can be complex to deconvolute because of various factors such as the system's size, temporal and spatial complexity, and allosteric behavior away from active sites. Relying solely on electron density map visualization can also pose a challenge in differentiating between useful and irrelevant data.

Metal-ligand delocalization of iron and cobalt porphyrin complexes in aqueous solutions probed by soft X-ray absorption spectroscopy.

Metal-ligand delocalization of metal porphyrin complexes in aqueous solutions was investigated by analyzing the electronic structure of both the metal and ligand sides using soft X-ray absorption spectroscopy (XAS) at the metal L-edges and nitrogen K-edge, respectively. In the N K-edge XAS spectra of the ligands, the energies of the CN π* peaks of cobalt protoporphyrin IX (CoPPIX) are higher than iron protoporphyrin IX (FePPIX). The energy difference between the two lowest peaks in the XAS spectrum of CoPPIX is also larger than that of FePPIX.

Thermal Energy Transport through Nonbonded Native Contacts in Protein.

Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of "communication" is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents.

Insight into the photodegradation of methylisothiazolinone and benzoisothiazolinone in aquatic environments.

Methylisothiazolinone (MIT) and Benzisothiazolinone (BIT) are two widely used non-oxidizing biocides of isothiazolinones. Their production and usage volume have sharply increased since the pandemic of COVID-19, inevitably leading to more release into water environment. However, their photochemical behaviors in water environment are still unclear.

Exploiting the Correlation between the 1s, 2s, and 2p Energies for the Prediction of Core-Level Binding Energies of Si, P, S, and Cl species.

The binding energies (BEs) of the 1s, 2s, and 2p core electrons of third-period elements (Si, P, S, Cl) were calculated using Hartree-Fock (HF) and B3LYP, BH&HLYP, and LC-BOP ΔSCF, and the shifted KS ΔSCF methods. Linear relationships between two BEs were derived and compared with the Auger parameter. The derived lines are essentially parallel, with only the intercepts differing.

New potential selective estrogen receptor modulators in traditional Chinese medicine for treating menopausal syndrome.

Women go through several predictable conditions and symptoms during menopause that are caused by age, changes in sex hormone levels, and other factors. Conventional menopause hormone therapy has raised serious concerns about the increased risks of cancers, blood clots, depression, etc. Selective estrogen receptor modulators (SERMs) that can be both agonists and antagonists of estrogen receptors in a tissue-specific manner are being developed to reduce the health concerns associated with menopause hormone therapy.

Computational evolution of social norms in well-mixed and group-structured populations.

Models of indirect reciprocity study how social norms promote cooperation. In these models, cooperative individuals build up a positive reputation, which in turn helps them in their future interactions. The exact reputational benefits of cooperation depend on the norm in place, which may change over time.

Long-range Corrected Density Functional Theory Including a Two-Gaussian Hartree-Fock Operator for High Accuracy Core-excitation Energy Calculations of Both the Second- and Third-Row Atoms (LC2gau-core-BOP).

In the previous work, LCgau-core-BOP, which includes the short-range interelectronic Gaussian attenuating Hartree-Fock (HF) exchange to the long-range HF exchange, showed high accuracy core-excitation energies from 1s orbitals of the second-row atoms (1s → π*, 1s → σ*, 1s → *, and 1s → Rydberg), but underestimates the core-excitation energies from 1s orbitals of the third-row atoms. To improve this, we added one more Gaussian attenuating HF exchange to LCgau-core-BOP. We named it LC2gau-core-BOP, which achieves a mean absolute error (MAE) of 0.