Biological Physics

New submissions

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New submissions for Fri, 17 May 24

[1]  arXiv:2405.09649 [pdf, other]

Title: Challenges and opportunities for digital twins in precision medicine: a complex systems perspective

Authors: Manlio De Domenico, Luca Allegri, Guido Caldarelli, Valeria d'Andrea, Barbara Di Camillo, Luis M. Rocha, Jordan Rozum, Riccardo Sbarbati, Francesco Zambelli

Subjects: Biological Physics (physics.bio-ph); Adaptation and Self-Organizing Systems (nlin.AO); Quantitative Methods (q-bio.QM)

The adoption of digital twins (DTs) in precision medicine is increasingly viable, propelled by extensive data collection and advancements in artificial intelligence (AI), alongside traditional biomedical methodologies. However, the reliance on black-box predictive models, which utilize large datasets, presents limitations that could impede the broader application of DTs in clinical settings. We argue that hypothesis-driven generative models, particularly multiscale modeling, are essential for boosting the clinical accuracy and relevance of DTs, thereby making a significant impact on healthcare innovation. This paper explores the transformative potential of DTs in healthcare, emphasizing their capability to simulate complex, interdependent biological processes across multiple scales. By integrating generative models with extensive datasets, we propose a scenario-based modeling approach that enables the exploration of diverse therapeutic strategies, thus supporting dynamic clinical decision-making. This method not only leverages advancements in data science and big data for improving disease treatment and prevention but also incorporates insights from complex systems and network science, quantitative biology, and digital medicine, promising substantial advancements in patient care.

[2]  arXiv:2405.10158 [pdf, other]

Title: Mechanics and morphology of proliferating cell collectives with self-inhibiting growth

Authors: Scott Weady, Bryce Palmer, Adam Lamson, Taeyoon Kim, Reza Farhadifar, Michael J. Shelley

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft)

We study the dynamics of proliferating cell collectives whose microscopic constituents' growth is inhibited by macroscopic growth-induced stress. Discrete particle simulations of a growing collective show the emergence of concentric-ring patterns in cell size whose spatio-temporal structure is closely tied to the individual cell's stress response. Motivated by these observations, we derive a multiscale continuum theory whose parameters map directly to the discrete model. Analytical solutions of this theory show the concentric patterns arise from anisotropically accumulated resistance to growth over many cell cycles. This work shows how purely mechanical processes can affect the internal patterning and morphology of cell collectives, and provides a concise theoretical framework for connecting the micro- to macroscopic dynamics of proliferating matter.

Cross-lists for Fri, 17 May 24

[3]  arXiv:2405.09646 (cross-list from cond-mat.soft) [pdf, other]

Title: Protein folding as a jamming transition

Authors: Alex T. Grigas, Zhuoyi Liu, Jack A. Logan, Mark D. Shattuck, Corey S. O'Hern

Comments: 5 pages, 4 figures

Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of $\phi_c=0.55$ found in experimental measurements. We show that as the hydrophobic interactions increase relative to the temperature, a novel jamming transition occurs when the core packing fraction exceeds $\phi_c$. The model also recapitulates the global structure of proteins since it can accurately refold to native-like structures from partially unfolded states.

[4]  arXiv:2405.10298 (cross-list from physics.plasm-ph) [pdf, other]

Title: Heavy-element damage seeding in proteins under X-ray free electron laser illumination conditions

Authors: Spencer K. Passmore, Alaric L. Sanders, Andrew V. Martin, Harry M. Quiney

Subjects: Plasma Physics (physics.plasm-ph); Biological Physics (physics.bio-ph); Computational Physics (physics.comp-ph)

The emerging technique of serial femtosecond X-ray crystallography (SFX) can be used to study the structure and dynamics of biological macromolecules to high spatial and temporal resolutions. An ongoing challenge for SFX is the damage caused by the ultrabright X-ray free electron laser pulse. Though it is often assumed that sufficiently femtosecond pulses `outrun' radiation damage, in reality electronic damage processes commence during exposure. We model the electronic damage to protein nanocrystals using a plasma model that tracks the continuous changes to the energy distribution of the unbound electrons. Tracking the continuous energy distribution is of particular importance for distinguishing the influence of differing elements on secondary damage processes. Heavy atoms have a ubiquitous but small presence in protein targets - typically as integral components of the macromolecule and as salts in the solvent. We find that these atoms considerably influence the simulated ionization and scattering behavior of realistic targets due to their rapid seeding of secondary ionization processes. In lysozyme, even the presence of native sulfur atoms significantly contributes to theoretical measures of damage-induced noise for >= 6 keV, 15 fs pulses. Contributing to the effect is that heavy atoms seed `intermediate' energy electron cascades that are particularly effective at ionizing the target on the femtosecond timescale. In addition, the disproportionate effect of heavy atoms means the damage to a protein crystal can be sensitive to their presence in the solvent. Outside of reducing the concentration of heavy atoms in the target, these results suggest the dose limits of SFX targets will be higher where the ionization of deep >~ 6 keV absorption edges is minimized, or, to a lesser extent, when such edges are only ionized with X-rays >> 2 keV above their binding energy.

[5]  arXiv:2405.10303 (cross-list from hep-ph) [pdf, other]

Title: Asymmetric Warm Dark Matter: from Cosmological Asymmetry to Chirality of Life

Authors: Wen Yin, Shota Nakagawa, Tamaki Murokoshi, Makoto Hattori

Comments: 22pages, 3figures, comments are welcome

Subjects: High Energy Physics - Phenomenology (hep-ph); Cosmology and Nongalactic Astrophysics (astro-ph.CO); Astrophysics of Galaxies (astro-ph.GA); Instrumentation and Methods for Astrophysics (astro-ph.IM); Biological Physics (physics.bio-ph)

We investigate a novel scenario involving asymmetric keV-range dark matter (DM) in the form of right-handed (sterile) neutrinos. Based on the Fermi-Dirac distribution, we demonstrate that asymmetric fermionic DM forms a Fermi degenerate gas, making it potentially colder than symmetric fermionic DM. This setup simultaneously accounts for the Universe's baryon asymmetry through tiny Yukawa interactions with Standard Model leptons and the Higgs field, and the homochirality of amino acids via decay into circularly polarized photons. This scenario can be investigated through soft X-ray searches conducted by current and upcoming space missions. The helical X-rays is a smoking-gun signal of our scenario. Additionally, we propose a new mechanism to suppress DM thermal production by introducing a light modulus, which may also benefit cosmology involving generic right-handed neutrinos with large mixing.

Replacements for Fri, 17 May 24

[6]  arXiv:2401.05878 (replaced) [pdf, ps, other]

Title: Protective Effect of Trehalose Sugar on Amyloid-Membrane Interactions using BLM Electrophysiology

Authors: Yue Xu, Carina Teresa Filice, Zoya Leonenko

Comments: This is an accepted manuscript to appear in the Biophysical Journal. The supplementary material was included at the end of the file

Subjects: Biological Physics (physics.bio-ph)

[7]  arXiv:2402.16711 (replaced) [pdf, other]

Title: Action potential propagation properties of 4D, 3D and 2D Hodgkin-Huxley type models

Authors: Lízia Branco, Rui Dilão

Comments: 8 pages, 11 figures

Subjects: Biological Physics (physics.bio-ph); Neurons and Cognition (q-bio.NC)

[8]  arXiv:2403.09386 (replaced) [pdf, other]

Title: Exploring the Interplay of Intrinsic Fluctuation and Complexity in Intracellular Calcium Dynamics

Authors: Athokpam Langlen Chanu, R.K. Brojen Singh, Jae-Hyung Jeon

Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Chaotic Dynamics (nlin.CD); Biological Physics (physics.bio-ph); Chemical Physics (physics.chem-ph)

[9]  arXiv:2405.06810 (replaced) [pdf, ps, other]

Title: Simulating Light Propagation through Biological Media Using Monte-Carlo Method

Authors: Maryam Ghahremani

Comments: arXiv admin note: text overlap with arXiv:1711.03244 by other authors

Subjects: Optics (physics.optics); Biological Physics (physics.bio-ph)

[10]  arXiv:2405.08489 (replaced) [pdf, ps, other]

Title: Effects of skull properties on transcranial focused ultrasound transmission

Authors: Han Li (1), Isla Barnard (1), Tyler Halliwell (1), Xinyu Zhang (2), Andreas Melzer (2), Zhihong Huang (1 and 2) ((1) School of Science and Engineering, University of Dundee, Dundee, UK,(2) School of Medicine, University of Dundee, Dundee, UK)

Comments: 31 pages, 8 figures

Subjects: Medical Physics (physics.med-ph); Biological Physics (physics.bio-ph)

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