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Category: mathematics

Open-source software unlocks rapid DNA structure generation and analysis in one workflow

Computational chemists at the University of Amsterdam’s Van ‘t Hoff Institute for Molecular Sciences have developed a comprehensive software suite to create accurate models of DNA in biomolecular assemblies. Called MDNA, the user-friendly molecular modeling toolkit helps biochemists, molecular biologists, bioinformaticians, and biophysicists to visualize and analyze DNA structures and perform accurate simulations.

The development of the MDNA suite, led by associate professor Jocelyne Vreede, has been presented in a paper in Nucleic Acids Research.

The software is open-source and publicly available through Figshare and Github. It is easily accessible, providing inspiration to any scientist with an interest in DNA. It has been thoroughly tested by students in mathematics, chemistry and biology, some of whom had hardly any programming experience.

Scientists identify a cell type in the brain that was previously ignored and it may explain why human memory has no known upper limit

The human brain contains roughly 86 billion neurons. That number appears in almost every popular account of memory and intelligence, and it tends to carry an implicit argument: that the scale of human cognition follows from the scale of this cell count. What is less often mentioned is that the brain contains a roughly comparable number of a different cell type entirely, one that researchers have treated, for most of the history of neuroscience, as little more than biological scaffolding.

A paper published on 23 May in the Proceedings of the National Academy of Sciences puts forward a new hypothesis about what those cells, called astrocytes, might actually be doing. The work comes from a team at MIT: lead author Leo Kozachkov, Jean-Jacques Slotine, a professor of mechanical engineering and brain and cognitive sciences, and Dmitry Krotov of the MIT-IBM Watson AI Lab, who is the paper’s senior author. Their claim is not that astrocytes have been misunderstood in any dramatic sense; it is the more careful suggestion that they may be doing computational work that neurons, on their own, cannot account for.

This is a hypothesis supported by a mathematical model. The experimental work needed to test it has not yet been done.

What If Scientists Already PROVED We’re In A Simulation?| Truth By Lisa Randall

If Scientists Already PROVED We’re In A Simulation?
Bell’s theorem. Maldacena’s holographic proof. Wheeler’s participatory universe.
Three independent bodies of peer-reviewed physics — all pointing at the same unsettling answer.
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Bell’s theorem. Maldacena’s holographic proof. Wheeler’s participatory universe.
Three independent bodies of peer-reviewed physics — all pointing at the same unsettling answer.
What if the simulation hypothesis isn’t a thought experiment? What if the physics we already have — quantum entanglement, the holographic principle, the measurement problem — is the proof?
In this video, Harvard theoretical physicist Lisa Randall walks through the three experiments and mathematical proofs that, taken together, describe a universe that functions in every measurable way like a simulation. Not as metaphor. As structure.
We cover:
→ Alain Aspect’s 1982 Bell test experiment and what it actually proved about local reality.
→ The Bekenstein-Hawking holographic bound — why information scales with surface area, not volume.
→ Maldacena’s AdS/CFT correspondence — the proof that a 3D universe is dual to a 2D information system.
→ Wheeler’s delayed choice experiment and the participatory universe.
→ What the fine-tuning problem looks like inside a simulation framework.
→ Why you — the observer — are not peripheral to the physics. You are part of the mechanism.
This is Episode 1 of The Proof Series — a weekly deep-dive into peer-reviewed science that challenges everything you think you know about reality.
New episode every Thursday.
— Lisa Randall is a theoretical physicist and professor at Harvard University, author of Warped Passages and Dark Matter and the Dinosaurs, and one of the most cited physicists alive.
#SimulationTheory #QuantumPhysics #HolographicUniverse.
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3. TIMESTAMPS / CHAPTERS
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00:00 — The proof nobody is talking about.
01:10 — What \

How a Richard Feynman formula could explain your dining habits in a new city

One of the dilemmas facing anyone in a new and unfamiliar city is where to dine out. You might consult guides, speak to locals, check reviews, and ultimately, try your luck. But if you’re there for a while, at some point you’re going to be asking yourself whether to visit new eateries or stick to the ones you’ve already tried and liked.

This is known as a classic explore-exploit dilemma and was something the late physicist and Nobel laureate Richard Feynman pondered during a restaurant meal with a friend in the 1970s. His companion was debating whether to order his favorite dish or try something new. Feynman turned the question into a math problem and solved it there and then, scribbling his workings on pieces of paper.

Feynman, who died in 1988, never published his solution, but researchers came across his handwritten notes and not only deciphered them, but also put the solution to the test.

Molecular glasses solve long-standing Arrhenius paradox

Glasses are non-crystalline but solid states of matter in which molecules and atoms are not arranged into a regular crystal lattice, but rather in a disordered pattern. Glassy materials are widely used in various settings, for instance, in the synthesis of pharmaceuticals and the development of electronics or optical devices.

When studying movement and changes in various materials and substances, physicists commonly rely on the so-called Arrhenius model. This is a mathematical framework introduced by Svante Arrhenius in 1889, which can be used to calculate how temperature affects the speed of a heat-activated chemical reaction or physical process.

Past studies have shown that when the Arrhenius model is applied to molecular glasses, it yields unrealistically small pre-exponential factors. Pre-exponential factors are values that describe the intrinsic timescale of the movement of molecules without considering temperature effects.

Predicting physics without parameter tuning: A faster computational approach

Numerical simulations in physics often require estimating a multitude of parameters, making the process computationally expensive and complex. Researchers at University of Tsukuba have introduced a new method called the multiparameter eigenvalue-problem emulator, enabling reliable predictions based directly on relationships among known data by eliminating the need for parameter estimation. This innovation considerably reduces computational costs and enables systematic quantification of predictive uncertainty.

Calibrating theoretical models with experimental data is a common practice in physics for predicting previously unobserved phenomena. However, real-world theoretical models are often highly complex, involving numerous numerical quantities, known as parameters, that cannot be directly measured. Researchers must estimate these parameters to compute other observables. This is a process that is computationally demanding and fraught with remarkable challenges in assessing how uncertainties in the parameters affect final predictions.

This study, published in Physical Review Letters, presents a novel fast surrogate model based on a mathematical framework known as the multiparameter eigenvalue-problem emulator. This model directly predicts unknown observables based on relationships among known data, without the need to introduce or estimate parameters.

E.W. Dijkstra Archive: On the cruelty of really teaching computing science (EWD 1036)

For Dijkstra, programming was closer to mathematics than to a craft. The goal wasn’t to “get a feel” for code. The goal was to reason about it rigorously, to understand why it works before discovering whether it works.

The second part of this talk pursues some of the scientific and educational consequences of the assumption that computers represent a radical novelty. In order to give this assumption clear contents, we have to be much more precise as to what we mean in this context by the adjective “radical”. We shall do so in the first part of this talk, in which we shall furthermore supply evidence in support of our assumption.

The usual way in which we plan today for tomorrow is in yesterday’s vocabulary. We do so, because we try to get away with the concepts we are familiar with and that have acquired their meanings in our past experience. Of course, the words and the concepts don’t quite fit because our future differs from our past, but then we stretch them a little bit. Linguists are quite familiar with the phenomenon that the meanings of words evolve over time, but also know that this is a slow and gradual process.

It is the most common way of trying to cope with novelty: by means of metaphors and analogies we try to link the new to the old, the novel to the familiar. Under sufficiently slow and gradual change, it works reasonably well; in the case of a sharp discontinuity, however, the method breaks down: though we may glorify it with the name “common sense”, our past experience is no longer relevant, the analogies become too shallow, and the metaphors become more misleading than illuminating. This is the situation that is characteristic for the “radical” novelty.

John Nash (1928−2015)

John Nash was born on June 13, 1928, in Bluefield, West Virginia, a former coal town nestled deep in the Appalachian Mountains. As a young boy, Nash was solitary, bookish, and introverted. His father, John Sr., was a quiet engineer with an incisive mind. His mother, Virginia, also intelligent, was a former teacher who had large dreams for her son, pushing him to read at four, learn Latin, and skip a grade at school.

The first hint of John Nash’s math talent came in fourth grade, when a teacher told Virginia that the boy couldn’t do the math. Virginia laughed, well aware that her son was going down his own path to solve the simple problems. In high school, John solved his teachers’ clunky proofs in just a few elegant steps. He was one of ten nationally awarded winners of the George Westinghose Award, which provided him with a full scholarship to the Carnegie Institute of Technology. He hopped from engineering to chemistry before discovering his passion: mathematics.

He was accepted into Princeton University, which at the time was to mathematicians what Detroit was, and still is, to cars. Nash first wowed his peers with an elegantly playable board game, which his peers dubbed “Nash,” but later reached the market as Hex. He then absorbed himself in one of the sexiest math fields of the day, game theory, which described strategies in competition, whether in card games or business. His deceptively simple doctoral thesis would later re-orient the field of economics, although no one, not even Nash, predicted its potential.

Mathematician solves origami donut efficiency challenge with fewest folds

Most people wouldn’t think that it would take rigorous mathematical proof to show how many folds it takes to make a donut shape out of paper. Yet, no one could quite figure it out until recently.

In a new paper, published in Proceedings of the National Academy of Sciences, mathematician Richard Evan Schwartz provides detailed proof of where the line is drawn when it comes to the fewest folds required to construct a torus—the proper name for the shape of a donut—from a piece of paper.

Better math discriminates exotic from classical materials

The planar Hall effect is a tabletop diagnostic tool for special quantum properties useful in basic research and technological applications. Or so it was thought, because careful calculation by Kobe University researchers clarifies the conditions under which this effect may also appear in classical materials. This makes the diagnostic more meaningful and enables more purposeful design.

In the hunt for materials with properties that are useful for quantum computing or spintronics, researchers have used the “planar Hall effect” as a tabletop diagnostic tool: The researchers send a current through a thin, flat sample and observe whether an electric voltage is produced in response to a magnetic field in the same plane as the sample.

If it is, the pattern of how the voltage responds to rotating the magnetic field in the plane of the sample tells researchers about the properties of the material.

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