arXiv subjects

Peyman Fahimi

Publications and source records attributed to Peyman Fahimi.

8 recordsLinked to original sources

arXiv2025

Decoding the Hot-Mitochondrion Paradox

In a 2018 paper and a subsequent article published in 2023, researchers reported that mitochondria maintain temperatures 10oC-15oC higher than the surrounding cytoplasm-a finding that deviates by five to six orders of magnitude from theoretical predictions based on Fourier's law of heat conduction. In 2022, we proposed a solution to this apparent paradox. In the present perspective, we build upon that framework and introduce new ideas to further unravel how a biological membrane-whether of an organelle or a whole cell-can become significantly warmer than its environment. We propose that ion-translocating proteins embedded in the inner mitochondrial membrane (IMM) can be modeled as ratchet engines, introducing a novel, previously overlooked mode of heat transfer. This mechanism, coupled with localized heat release during the cyclical dehydration-translocation-hydration of ions through membrane proteins, may generate transient but substantial temperature spikes. The cumulative thermal occupancy of these microscopic events across the three-dimensional surface of the IMM can account for the elevated temperatures detected by molecular probes.

q-bio.SC↗

arXiv2025

Rotational Dynamics of ATP Synthase: Mechanical Constraints and Energy Dissipative Channels

The proton motive force (PMF) across the inner mitochondrial membrane delivers approximately 0.2 eV of energy per proton, powering the FoF1-ATP synthase molecular motor. Here, we provide a detailed accounting of how this energy is utilized: Approximately 75-83% is transduced into the chemical free energy of ATP synthesis, while the remaining 17-25% is dissipated through internal friction, viscous drag, proton leakage, electroviscous effects, elastic deformations, and information-theoretic costs. Each dissipation channel is quantitatively evaluated, revealing that internal friction in the F1 motor is the dominant loss mechanism. In this work, we did not account for the energy supplied/injected due to the intrinsic electrostatic potential of the enzyme itself. In addition to this energy bookkeeping, we also examine the quantum mechanical constraints on the Fo unit's rotation. We find that, as can be expected, the energy spacing between quantized rotational states is several orders of magnitude smaller than thermal energies at physiological temperature, and that the tunneling probability through rotational barriers practically totally non-existent. Furthermore, the biological rotation speed (100-650 revolutions per second (rps)) is between one and three orders of magnitude below the quantum limit implied by quantization of angular momentum of the c-ring (which would have been ca. 13,000 to 62,000 rps (depending on the size of the c-ring (17 to 8 subunits, respectively)) in the first rotational energy level of the c-ring). Nevertheless, experimental estimates of the rotation rates in isolated c-ring suggest rates in the vicinity of 43,000 rps, right within our theoretical quantum estimates. However, ATP synthase as a whole operates firmly within the classical regime, despite its nanoscale dimensions, and highlight its evolutionary optimization for robust and efficient energy conversion....

q-bio.BM↗

arXiv2025

Costs and benefits of phytoplankton motility

The motility skills of phytoplankton have evolved and persisted over millions of years, primarily in response to factors such as nutrient and light availability, temperature and viscosity gradients, turbulence, and predation pressure. Phytoplankton motility is broadly categorized into swimming and buoyancy regulation. Despite studies in the literature exploring the motility costs and benefits of phytoplankton, there remains a gap in our integrative understanding of direct and indirect energy expenditures, starting from when an organism initiates movement due to any biophysical motive, to when the organism encounters intracellular and environmental challenges. Here we gather available pieces of this puzzle from literature in biology, physics, and oceanography to paint an overarching picture of our current knowledge. The characterization of sinking and rising behavior as passive motility has resulted in the concept of sinking and rising internal efficiency being overlooked. We define this efficiency based on any energy dissipation associated with processes of mass density adjustment, as exemplified in structures like vacuoles, gas vesicles, and frustules. We propose that sinking and rising are active motility processes involving non-visible mechanisms, as species demonstrate active and rapid strategies in response to turbulence, predation risk, and gradients of nutrients, light, temperature, and viscosity. In swimmers, internal and external motility efficiencies have been extensively explored in theoretical studies, yet they are largely neglected in energetic estimates within marine and freshwater sciences. Identifying the dissipative processes associated with swimming and buoyancy-regulating machinery offers deeper insight into motility costs relative to an organism's total metabolic rate.

physics.bio-ph↗

arXiv2024

The sounds of science a symphony for many instruments and voices part II

Despite its amazing quantitative successes and contributions to revolutionary technologies, physics currently faces many unsolved mysteries ranging from the meaning of quantum mechanics to the nature of the dark energy that will determine the future of the Universe. It is clearly prohibitive for the general reader, and even the best informed physicists, to follow the vast number of technical papers published in the thousands of specialized journals. For this reason, we have asked the leading experts across many of the most important areas of physics to summarise their global assessment of some of the most important issues. In lieu of an extremely long abstract summarising the contents, we invite the reader to look at the section headings and their authors, and then to indulge in a feast of stimulating topics spanning the current frontiers of fundamental physics from The Future of Physics by William D Phillips and What characterises topological effects in physics? by Gerard t Hooft through the contributions of the widest imaginable range of world leaders in their respective areas. This paper is presented as a preface to exciting developments by senior and young scientists in the years that lie ahead, and a complement to the less authoritative popular accounts by journalists.

physics.soc-ph↗

arXiv2023

Binary Color-Coded Magic Squares: A Study of Uniqueness Under Rotation/Reflection, PCA, and LDA Analysis

In this paper, we study the concept of "binary color-coded magic squares" by assigning two distinct colors to the even and odd numbers within a magic square. We investigate the uniqueness of patterns within these squares using three different analytical methods, including rotation/reflection, PCA, and LDA. Our investigation covers all 880 magic squares of order 4, all 48,544 associative magic squares of order 5, and all 368,640 Franklin magic squares of order 8. Our investigation reveals striking patterns that were previously unknown in traditional magic squares, shedding light on the potential for binary color-coded magic squares to contribute to the field of mathematics.

math.GM↗

arXiv2023

A Travelling Salesman Paths within nxn (n = 3, 4, 5) Magic Squares

Intriguing symmetries are uncovered regarding all magic squares of orders 3, 4, and 5, with 1, 880, and 275,305,224 distinct configurations, respectively. In analogy with the travelling salesman problem, the distributions of the total topological distances of the paths travelled by passing through all the vertices (matrix elements) only once and spanning all elements of the matrix are analyzed. Symmetries are found to characterise the distributions of the total topological distances in these instances. These results raise open questions about the symmetries found in higher-order magic squares and the formulation of their minimum and maximum total path lengths.

math.GM↗

arXiv2022

ATP Synthase: A Moonlighting Enzyme with Unprecedented Functions

ATP synthase's intrinsic molecular electrostatic potential (MESP) adds constructively to, and hence reinforces, the chemiosmotic voltage. This ATP synthase voltage represents a new free energy term that appears to have been overlooked. This term is at least roughly equal in order of magnitude and opposite in sign to the energy needed to be dissipated as a Maxwell's demon (Landauer principle).

physics.bio-ph↗

arXiv2021

The Hot Mitochondrion Paradox: Reconciling Theory and Experiment

Experiments by Chretien and co-workers suggest that mitochondria are 10oC hotter than their surroundings. Steady-state theoretical estimates place this difference at a maximum of 10^-5 oC. This million-fold disagreement may be called the hot mitochondrion paradox. It is suggested that every proton translocated via ATP synthase sparks a picosecond temperature-difference spike of the order of magnitude measured by Chretien et al. Time-averaging of these spikes recovers the theoretical value. Further, a temporal and spatial superposition of the fluorescence intensity of a very large number of molecular thermometer molecules in the sample can give the appearance of a steady signal. The inner mitochondrial membrane appears to be flanked by temperature differences fluctuating in time and along the membrane s surface, with hot and cold spots as ultrashort temperature spikes.

physics.bio-ph↗