[Computer simulation of protein molecular dynamics]. A review of the works on the computer simulation of the globular protein dynamics is given. Methodological aspects of the simulation procedure are outlined briefly. Main peculiarities of protein dynamics revealed in the course of simulation of pancreatic trypsin inhibitor and cytochrome c are presented. The causes of "anomalous" processes, inherent in the simulated behaviour of model proteins are discussed. These "anomalous" processes are: continuous drift of the structure and its deviation from the experimental one, determined by X-ray analysis. Both processes are supposed to be the consequence of the reduced conformational rigidity of the model protein in comparison to the real one. Among the possible reasons for this reduced rigidity absence of the water molecules, hydrating peptide groups in the real protein, may be mentioned. Analogy between "anomalous" processes in the simulated protein dynamics and some phenomena observed in the real proteins during their functioning is drawn. Published in Molekuliarnaia biologiia

Physics-based animation is a multidisciplinary area that uses ideas from physics, computer science, and mathematics to create realistic and dynamic movements in virtual settings. The basic ideas and methods of physics-based animation are introduced in this research paper, with an emphasis on how mathematical models and physical laws are used to produce realistic motion in computer-generated images. To construct realistic virtual environments, key disciplines covered include fluid simulation, fabric simulation, rigid body dynamics, and soft body dynamics. The report highlights recent developments in real-time physics simulations and addresses other topics such as processing economy, accuracy, and scalability. Applications for physics-based animation can be found in many different fields, such as virtual reality, simulation training, movies, and video games. The pursuit of more precise and effective physics-based animation is essential as technology develops to produce captivating and realistic virtual worlds. Keywords— Physics-based animation(PBA), virtual environment, Physics simulation, Dynamics, Animation software, Real-time physics, Collision detection, Fluid dynamics, Particle systems, Cloth simulation, Smooth particle hydrodynamics, finite element method, Navier-Stokes, Rigid body dynamics, Soft body dynamics, Deformation, Motion capture, Character animation, Kinematics, Rendering, Game development, Virtual reality, Augmented reality, Computer graphics, Simulation accura

Using Computer Simulation to Effectively Solve Power... Skip to main content Have a personal or library account? Click here to login Using Computer Simulation to Effectively Solve Power Transmission Problems for Non-Sinusoidal Waveforms Acta Mechanica et Automatica Volume 19 (2025): Issue 3 (September 2025) By:  Maciej KLEBBA ,   Arkadiusz FRĄCZ ,   Michał BRODZICKI   and   Adrianna RZEPKOWSKA     Open Access | Sep 2025 Download Download Abstract Abstract Nonlinear and periodically switched receivers can cause distortions in current and voltage waveforms within power systems. The growing use of renewable energy sources introduces electrical energy into the system through power converters, which often produce voltages that approximate a sinusoidal waveform rather than being perfectly sinusoidal. This trend poses increasing challenges in designing new systems and managing existing ones. A proper description and interpretation of the physical phenomena associated with non-sinusoidal waveforms have become increasingly important. This paper presents simulation models of power circuits using non-sinusoidal signals and discusses the energy transfer that occurs within them. It also outlines current computational methods based on circuit theories as they apply to these systems. The results from the calculations and simulations in various configurations are compared with data obtained from real objects. The findings highlight fundamental inaccuracies in the methods used and potential errors arising from computer simulations. Preview Download Article Figures & tables References Authors Metrics Articles in this issue DOI:  https://doi.org/ 10.2478/ama-2025-0043 | Journal eISSN:  2300-5319 | Journal ISSN:  1898-4088 Journal RSS Feed Language:  English Page range:  362 - 368 Submitted on:  Feb 7, 2025 | Accepted on:  Jun 10, 2025 | Published on:  Sep 5, 2025 Published by:  Bialystok University of Technology In partnership with:  Paradigm Publishing Services Keywords: energy transfer , non-sinusoidal waveforms , distortion , simulation , reactive power , power factor Related subjects: Engineering , Mechanical engineering , Mechanics , Engineering , Bioengineering and biomedical engineering , Biomechanics , Engineering , Civil engineering , Environmental engineering © 2025 Maciej KLEBBA, Arkadiusz FRĄCZ, Michał BRODZICKI, Adrianna RZEPKOWSKA , published by Bialystok University of Technology This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License .

may be used in Computer simulations to model real-world phenomena and predict outcomes. The simulation hypothesis is the view that the whole world and Reality is the totality of existence or what all existing entities have in common. It is often contrasted with appearance, opposing what is with what seems to be, although the accuracy and fundamentality of this contrast are disputed. Various criteria for distinguishing real from unreal entities have been proposed, including causal powers, mind-independence, and being non-illusory. The concept of Ep… On this view, higher levels show greater complexity and new phenomena but depend on the lower ones and could not exist without them. Lower levels, by contrast, operate according to more basic mechanisms and are prior to the higher ones. In this sense, there can be matter without biological life, whereas life is built upon matter and depends on it. Non-reductive physicalists hold that everything is ultimately physical while insisting that higher-level psychological facts cannot be reduced to fundamental physics. According to this view, even a complete understanding of physics would not render sciences dedicated to higher levels, such as psychology, obsolete. Absolutists and relationalists discuss whether spacetime is itself a distinct object, such as a huge container, or a network of relations between objects. Eternalism is the view that past, present, and future are equally real. It contrasts with the growing block universe theory, which claims that the future is not real, and with presentism, which holds that only the present is real. The concept of causality describes relations between entities in spacetime. It links causes and effects as entities interact and influence each other, as when a thrown rock is the cause and a shattered window the effect. Phenomenalism, a related view, reduces physical objects to collections of actual or possible sensory experiences. Relativism, another form of anti-realism, holds that what counts as real varies based on one's perspective or conceptual framework. Constructivism asserts that reality is constructed rather than discovered. Quietism takes a different approach by seeking to undermine the discussion between realism and anti-realism. It holds that the debate is not based on a substantive disagreement but arises instead from conceptual confusions. Constructive empiricism, a closely related view, holds that scientific theories aim at empirical adequacy rather than full truth and may employ theoretical posits as long as they produce accurate descriptions of observable phenomena. Local realism is a view that combines the principle of locality with the notion that there are definite physical properties, whether or not they are being observed by someone. The principle of locality is the idea that physical objects are influenced only by their immediate surroundings: there is no direct or instantaneous action at a distance; all interactions occur and propagate through local mechanisms. Direct and indirect realism are different ways of understanding the relation between the objects in perceptual experience and the physical objects causing them. According to direct realism, there is no essential difference: the experienced objects are the real objects, implying a direct connection between perception and reality. A challenge for direct realism comes from erroneous perceptions, such as illusions, in which experienced entities do not correspond to real ones. Indirect realism seeks to resolve this problem by distinguishing between the mental entities involved in perception and the physical entities that cause them. The reality–virtuality continuum is a theoretical framework that posits a continuous scale of mixed reality forms. For example, augmented reality devices may provide only sparse cues or overlay dense layers of digital content. Similarly, virtual reality worlds may incorporate real-world objects into the simulation or be entirely virtual. Various philosophical problems are associated with the ontological status of virtual objects, such as a magic sword found inside a video game world. One perspective holds that such objects are illusory or unreal because they lack existence in the physical world outside the simulation. Various other subfields of philosophy examine specific domains of reality. For example, value theory is concerned with the reality of values, and the philosophy of mathematics explores in what sense mathematical objects, like numbers and sets, form part of reality. In the sciences, physics studies the physical world and encompasses a broad range of phenomena. At the subatomic scale, particle physics focuses on elementary particles and their interactions. At the astronomical scale, cosmology analyzes the origin, structure, and development of the universe as a whole. Reality testing is another suggested psychological function in which individuals distinguish intrapsychic from external events to assess how their experience aligns with reality. Computer scientists discuss how systems of knowledge representation can organize information about reality and make it accessible to computational processes. Such data may be used in Computer simulations to model real-world phenomena and predict outcomes. The simulation hypothesis is the view that the whole world and everything within it is a simulated reality, including humans. A related idea holds that information is the fundamental substance of reality. Inspired by Leibniz, David Lewis (1941–2001) developed modal realism, maintaining that possible worlds are as real as the actual world. In physics, Albert Einstein (1879–1955) developed the theory of relativity, which treats space and time as interwoven dimensions whose geometry is curved by matter and energy. Quantum mechanics originated in the works of Niels Bohr (1885–1962), Werner Heisenberg (1901–1976), and Erwin Schrödinger (1887–1961).

First-hand experiences in several design projects that were based on media richness and collaboration are described in this article. Although complex design processes are merely considered as socio-technical systems, they are deeply involved with natural systems. My collaborative research in the field of performance-oriented design combines digital and physical conceptual sketches, simulations and prototyping. GIGA-mapping - is applied to organise the data. The design process uses the most suitable tools, for the subtasks at hand, and the use of media is mixed according to particular requirements. These tools include digital and physical GIGA-mapping, parametric computer aided design (CAD), digital simulation of analyses, as well as sampling and 1:1 prototyping. Also discussed in this article are the methodologies used in several design projects to strategize these tools and the developments and trends in the tools employed. The paper argues that the digital tools tend to produce similar results through given pre-sets that often do not correspond to real needs. Thus, there is a significant need for mixed methods including prototyping in the creative design process. Media mixing and cooperation across disciplines is unavoidable in the holistic approach to contemporary design. This includes the consideration of diverse biotic and abiotic agents. I argue that physical and digital GIGA-mapping is a crucial tool to use in coping with this complexity. Furthermore, I propose the int

Electrophoresis: mathematical modeling and computer simulation. A mathematical model of electrophoretic separation processes has been developed and adapted for computer simulations. The model is used to predict the characteristic behavior of a variety of electrophoretic techniques from a knowledge of chemical equilibria and physical transport phenomena. The model provides a unifying basis for a rational classification of all electrophoretic processes. Published in Science (New York, N.Y.) (1983)

A quantum computer is a computer that represents and processes information using quantum states. Quantum computations exploit phenomena such as superposition A quantum computer is a computer that represents and processes information using quantum states. Quantum computations exploit phenomena such as superposition, interference, and entanglement. Quantum computers have the potential to complete some calculations exponentially faster than classical computers. For example, a large-scale quantum computer could break widely used encryption schemes and aid A quantum computer is a computer that represents and processes information using quantum states. Quantum computations exploit phenomena such as superposition, interference, and entanglement. Quantum computers have the potential to complete some calculations exponentially faster than classical computers. For example, a large-scale quantum computer could break widely used encryption schemes and aid physicists in performing physical simulations. However, current hardware implementations of quantum computation are largely experimental and suitable for only certain specialized tasks. The basic unit of information in quantum computing, the qubit (quantum bit), serves a similar function as the bit in ordinary or "classical" computing. Unlike a classical bit, which can be in one of two states (a binary), a qubit can exist in a linear combination of states known as a quantum superposition. The result of measuring a qubit is one of the two states, given by a probabilistic rule. If a quantum computer manipulates the qubit in a particular way, wave interference effects amplify the probability of the desired measurement result. Quantum algorithm design involves creating procedures that allow a quantum computer to perform this amplification. Quantum computers are not yet practical for real-world applications. If a physical qubit is not sufficiently isolated from its environment, it suffers from quantum decoherence, introducing noise (error) into calculations. Governments have invested in research aimed at developing qubits with longer coherence times and lower error rates. Example implementations include superconductors (which isolate an electrical current by eliminating electrical resistance) and ion traps (which confine a single atomic particle using electromagnetic fields). Researchers have claimed that quantum devices can outperform classical computers on specific tasks, a metric referred to as quantum advantage or quantum supremacy. Such tasks are not necessarily useful for real-world applications. As a result, as of 2026 demonstrations are best understood as scientific milestones rather than evidence for near-term deployment. Global government investment in quantum…

Thin and slender structures are widely occurring both in nature and in human creations. Clever geometries of thin structures can produce strong constructions while using a minimal amount of material. Computer modeling and analysis of thin and slender structures has its own set of problems stemming from assumptions made when deriving the equations modeling their behavior from the theory of continuum mechanics. In this thesis we consider two kinds of thin elastic structures; threads and plates. Real-time simulation of threads are of interest in various types of virtual simulations such as surger

Organoids are self-organizing multicellular structures generated in vitro that recapitulate the micro-architecture and function of an organ. They are commonly derived from stem cells but can also emerge from pieces of proliferative tissues. Organoid technology has opened novel ways to model development and disease, but it is not without challenges. Computational models of organoids have been established to elucidate organoid growth and facilitate the optimization of organoid cultures. This article is a systematic review of in silico organoid models constructed at single-cell or subcellular resolution. PubMed, Scopus, and Web of Science were searched for original papers published in peer-reviewed journals before 26 September 2025, yielding 439 records after deduplication. Two independent reviewers screened their titles and abstracts, retrieved 84 papers for full-text scrutiny, and identified 32 papers that met the inclusion criteria. They were grouped by organoid type: 12 intestinal, 1 airway, 2 pancreas, 3 neural, 1 kidney, 1 inner cell mass, 9 tumor, and 3 generic. The analysis of these works revealed that computer simulations guided experimental work. Parsimonious computational models provided insights into diverse organoid behaviors, such as the rotation of airway organoids, size oscillations of pancreatic organoids, epithelial patterning of neural tube organoids, or nephron segment formation in kidney organoids. Generally, a deep understanding was achieved through combined in silico and in vitro investigations (e.g., optic cup morphogenesis). Recent research trends suggest that next-generation computational models of organoids may emerge from a more detailed understanding of the complex regulatory circuits that govern stem cell fate, and machine-learning-based, high-throughput imaging of organoids.

<h4>Rationale</h4>Lyon and coworkers demonstrated that multiple random fragmentation events can bias intensity distributions toward smaller terminal fragment ions. With any high-yield method of dissociation, such as high-energy collisional activation, this phenomenon can greatly influence the intensity distribution of product ions in MS/MS spectra. Previously, multiple fragmentation events were simulated with computationally intensive stochastic studies. The goal of this work is to provide a mathematical model that explains the results obtained from computational stochastic studies.<h4>Methods</h4>We present a probabilistic model that predicts terminal and internal product ion intensities based on polypeptide size and the number of fragmentation events. This model is validated by demonstrating convergence with the previous stochastic model and described that the intensity trend from smaller fragments to larger fragments follows the probability of multiple fragmentation events on peptide backbone.<h4>Results</h4>Under the stated assumptions, the analytical expressions formally demonstrate that the "missing middle" is a necessary mathematical consequence of multiple fragmentation events, and they reproduce the stochastic simulation results with exact agreement while reducing computation time from hours to less than 1 s. Our method consistently offers greater accuracy and mathematically proves the mechanistic necessity of "missing middle" phenomenon in top-down MS. The abundances of fragments from stochastic simulation distribute around the average value calculated by the probability formula within twofold coefficient variance (%CV).<h4>Conclusion</h4>The closed-form probability expressions accurately describe the combinatorial consequences of multiple fragmentation events under the stated assumptions. Because they are computationally inexpensive and differentiable, these expressions could be integrated with sequence-dependent fragmentation propensities in future machine learning models for MS/MS spectral prediction.

Oryx Simulations develops and manufactures real-time physics simulators for training of harbor crane operator in several of the world’s major harbors. Currently, the modelling process is labor-intensive and a faster solution that can produce accurate, textured models of harbor scenes is desired. The accuracy requirements vary across the scene, and in some areas accuracy can be traded for speed. Due to the heavy equipment involved, reliable error estimates are important throughout the scene. This report surveys the scientific literature of 3D reconstruction algorithms from aerial and terrestria