Chemical computer

If measured from beginning to end, the DNA in our cells is too long to fit into the cell's nucleus, explaining why it must be constantly folded and packaged. When it is time for cell division, and the genetic information needs to be passed on to the next generation, DNA must be packed particularly tightly, or else serious consequences for a cell's viability might ensue.

About 100 cells divide every second in our body. A key protein in cell division is a protein kinase termed Plk1, because it activates other proteins involved in this process. Plk1 is also overexpressed in many types of cancer. This makes it a promising target for cancer therapies. However, drugs that inhibit Plk1 have often proven ineffective.

Professor Kwang-Hyun Cho's research team of the Department of Bio and Brain Engineering at KAIST has captured the critical transition phenomenon at the moment when normal cells change into cancer cells and analyzed it to discover a molecular switch hidden in the genetic network that can revert cancer cells back into normal cells.

Treating hair loss may be as simple as developing therapies to flip a molecular "switch," according to a new study by researchers from Penn State; the University of California, Irvine; and National Taiwan University.

Researchers swap nitrogen and boron into DNA to create analogues that are geometrically and electrostatically equivalent to conventional DNA

Researchers at Kyushu University have revealed how spatial distance between specific regions of DNA is linked to bursts of gene activity. Using advanced cell imaging techniques and computer modeling, the researchers showed that the folding and movement of DNA, as well as the accumulation of certain proteins, changes depending on whether a gene is active or inactive.

Protein biosynthesis—the process whereby cells produce protein molecules, which are essential for life and growth—is a highly complex and strictly regulated affair. An interdisciplinary team led by LMU biologist PD Dr. Jürgen Lassak has now discovered a previously unknown mechanism by which bacteria control this process.

A living cell is a bustling metropolis, with countless molecules and proteins navigating crowded spaces in every direction. Cell division is a grand event which completely transforms the landscape. The cell starts behaving like the host of an international competition, reconfiguring entire streets, relocating buildings and rerouting its transportation systems.

Liquid crystals exist in a phase of their own. They can flow like liquids, but because their molecules are arranged in a somewhat orderly way, they can be easily manipulated to reflect light. This flexibility has made liquid crystals the go-to material for energy-efficient phone, TV, and computer display screens.

Computers made from DNA have previously only been able to store information or perform computations on it – now a new device can do both

The mTORC1 signaling pathway senses nutritional information and influences craniofacial development in mice.

Molecular computer components could represent a new IT revolution and help us create cheaper, faster, smaller, and more powerful computers. Yet researchers struggle to find ways to assemble them more reliably and efficiently.

Artificial DNA sorts images like a neural network does

The Belousov-Zhabotinsky reaction powers cellular automata and optimisation calculations

The new processor stores data in modified DNA molecules and uses microfluidic channels to perform basic computations.

Blocking an abnormally active signaling pathway in skeletal stem and progenitor cells alleviates bone mass decline in middle-aged mice. 

A new computer program allows scientists to design synthetic DNA segments that indicate, in real time, the state of cells. It will be used to screen for anti-cancer or viral infections drugs, or to improve gene and cell-based immunotherapies.

All the cells in our body have the same genetic code, and yet they can differ in their identities, functions and disease states. Telling one cell apart from another in a simple manner, in real time, would prove invaluable for scientists trying to understand inflammation, infections or cancers.

A new computer program allows scientists to design synthetic DNA segments that indicate, in real time, the state of cells. It will be used to screen for anti-cancer or viral infections drugs, or to improve gene and cell-based immunotherapies.

Blocking an abnormally active signaling pathway in skeletal stem and progenitor cells alleviates bone mass decline in middle-aged mice. 

Bacteria of the genus Shigella, closely related to the well-known Escherichia coli, are the second most common cause of fatal bacterial diarrheal diseases, with over 200,000 victims worldwide every year. There are repeated outbreaks of strains that are resistant to common antibiotics.

A conventional computer must be fully assembled before it can run, but an experimental DNA computer solves problems through the very act of putting itself together

A molecular switch, or molecule that changes in response to varying environmental stimuli, has successfully modified the acidity of a zeolite catalyst to improve the yield of paraxylene from methanol in heterogeneous catalysis, or a reaction where the catalyst, or molecule that facilitates a chemical reaction, and the reactants are in different phases, such as liquid and solid.

Battery research tool lets researchers extract pixel-by-pixel information from nanoscale X-ray movies of electrode particles absorbing and releasing

It lets researchers extract pixel-by-pixel information from nanoscale X-ray movies of electrode particles absorbing and releasing lithium ions. 

Mixing and matching various strands of DNA can create versatile biological computer circuits that can take the square roots of numbers or solve quadratic equations

Our body's fat metabolism plays a vital role in energy production in our body. A research team at the University of Basel, Switzerland, has discovered a molecular switch that regulates lipid metabolism in our cells. This switch controls the storage or conversion of lipids into energy.

Why do some animals regenerate lost tissues after injury while others don't? Researchers from the lab of Kerstin Bartscherer (Osnabrück University and formerly Hubrecht Institute) and Ashley Seifert (University of Kentucky) studied spiny mice, which have a remarkable regenerative capacity, to answer this question. They compared and modulated the injury responses of these mice and common laboratory mice, that show scarring upon injury. This revealed that ERK signaling is a crucial molecular switch between scarring and regeneration.

Simple calculations, such as factorising low numbers, can be made by mixing together differently shaped strands of DNA

A research team led by Professor Byung-Chang Suh has investigated the real-time effect of the G-protein cycle, which acts as a switch in the body, on the structural changes in G protein-coupled receptors (GPCRs). Their study is published in the journal Nature Communications.

In the inner ear, there are two different types of sensory cells that are responsible for hearing. An MHH research team has now identified the molecular switch for the formation of these inner and outer hair cells and thus found an important building block for the treatment of hearing loss.

Researchers at the John Innes Centre and partners at the Chinese Academy of Sciences have identified a molecular switch that establishes differential cell growth and organ shape.

A key protein for converting adult stem cells into cells that resemble embryonic stem cells has been visualized in unprecedented detail by an international team of researchers around Hans Schöler and Vlad Cojocaru of the Max Planck Institute for Molecular Biomedicine in Münster. By combining experiments and computer simulations, the team visualized how the Oct4 protein binds and opens short pieces of DNA while wrapped around nuclear storage proteins (histones), just like in our genome. The results were published in the journal Nucleic Acids Research on September 22.

This molecule tells the brain whether to put a positive or negative spin on events. Mental disorders may result when the up/down labeling goes awry.

University of Queensland scientists have cracked a problem that's frustrated chemists and physicists for years, potentially leading to a new age of powerful, efficient, and environmentally friendly technologies.

A chemical computer can now be programmed to solve concrete problems. The way it performs calculations is closer to a brain than a traditional computer so may help researchers to better understand how brains work

An international team of researchers has developed a computer system that can analyze a sample of chemical waste and create the routes to synthesize new, useful chemicals. In their paper published in the journal Nature, the group describes the work that went into creating the system and how well it worked when they tested it by synthesizing chemicals from waste samples.

Chemists integrated computer functions into rolling DNA-based motors, opening a new realm of possibilities for miniature molecular robots.

Chemists integrated computer functions into rolling DNA-based motors, opening a new realm of possibilities for miniature, molecular robots. These DNA-based motors combine computational power with the ability to burn fuel and move in an intentional direction.

The motors can sense chemical information in their environment, process that information, and then respond accordingly, mimicking some basic properties of living cells.

A trio of researchers at Emory University has found a way to speed up parallel processing in a DNA computer. In their paper published in the journal Nature Nanotechnology, Selma Piranej, Alisina Bazrafshan and Khalid Salaita describe how they applied DNA as a coating on glass beads and used the results as a type of DNA computer.

A device made from glass microbeads could offer 100 times more processing power than other DNA computers

Genetic networks mimic electronic circuits to perform a range of logic functions. Northwestern University synthetic biologists have developed

A simple test for water pollution involving engineered strands of DNA can report levels of contamination, and this biological system can carry out logical operations like those done by computers

Synthetic biologists have developed a low-cost, easy-to-use, hand-held device that can let users know -- within mere minutes -- if their water is safe to drink. The new device works by using powerful and programmable genetic networks, which mimic electronic circuits, to perform a range of logic functions.

Synthetic biologists have developed a low-cost, easy-to-use, hand-held device that can let users know - within mere minutes - if their water is safe to drink.

Northwestern University synthetic biologists have developed a low-cost, easy-to-use, hand-held device that can let users know—within mere minutes—if their water is safe to drink.

A molecular switch influences addiction behavior and determines how strong the response to addictive drugs is. A research team made the discovery in mice treated with cocaine. The researchers demonstrated that the protein Npas4 regulates the structure and function of nerve cells that control addiction behavior in mice. If the quantity of Npas4 was reduced in an experiment, the animals' response to cocaine was much weaker.

New research demonstrates a metabolic regulatory molecule called Them1 prevents fat burning in cells by blocking access to their fuel source. The study may contribute to the development of a new type of obesity treatment.

Linked to serious health problems including cancer, diabetes and cardiovascular disease, obesity affects more than a third of

Getting energy and nutrients from the environment—eating—is such an important function that it has been regulated through sophisticated mechanisms over hundreds of millions of years. Some of these mechanisms are only now beginning to be unraveled. A group at the Spanish National Cancer Research Centre (CNIO) has found one of their key components—a switch that controls the ability of organisms to adapt to low cellular nutrient levels.

Researchers from the Hubrecht Institute in Utrecht (The Netherlands) and the Max Planck Institute for Molecular Biomedicine in Münster (Germany) used computer simulations to reveal in atomic detail how a short piece of DNA opens while it is tightly wrapped around the proteins that package our genome. These simulations provide unprecedented insights into the mechanisms that regulate gene expression. The results will be published in PLOS Computational Biology on 3 June.

Jumping movement is commonly observed in nature, including for mammals, insects and the other land creatures; this fluid motion aims for rapid mobility, a faster arrival time at a destination over large obstacles and rough terrain. The qualitative properties of the jump such as direction and height are regulated by mere fractions of potential and kinetic energy. In addition, an organism can opt to repeat its jumping motions as decided by its own free will.

Kidney development is a balancing act between the self-renewal of stem and progenitor cells to maintain and expand their numbers, and the differentiation of these cells into more specialized cell types. Scientists demonstrates the importance of a molecule called beta-catenin in striking this balance.

In the past few years, researchers have turned increasingly to data science techniques to aid problem-solving in organic synthesis.

Scanning probe microscopes like the scanning tunneling microscope and the atomic force microscope give researchers valuable information about individual molecules. One of the most interesting areas of research is molecular switches, which can be switched from one configuration to another.

Researchers have developed a groundbreaking method to detect the dynamics of light on such a small scale with high temporal resolution.

A team of researchers with Google's AI Quantum team (working with unspecified collaborators) has conducted the largest chemical simulation on a quantum computer to date. In their paper published in the journal Science, the group describes their work and why they believe it was a step forward in quantum computing. Xiao Yuan of Stanford University has written a Perspective piece outlining the potential benefits of quantum computer use to conduct chemical simulations and the work by the team at AI Quantum, published in the same journal issue.

NUS biologists discovered the mobile TERMINAL FLOWER1 (TFL1) protein as an essential molecular switch for regulating endosperm development and seed size.

Around 1 billion people on the planet are infected with parasitic helminths, round worms that live in soil and colonize human guts through dirty water. The helminths owe their ability to survive in the low oxygen environment of the human gut to a unique enzyme variant, Donnelly Centre researchers have found.

Molecular switches are the molecular counterparts of electrical switches and play an important role in many processes in nature. Nanotechnologist now produced a photographic film at the atomic level and thus tracked the motion of a molecular building block. The result was a light-controlled 'pedalo-type motion', going forward and backward.

Molecular switches—they are the molecular counterparts of electrical switches and play an important role in many processes in nature. Such molecules can reversibly interconvert between two or more states and thereby control molecular processes. In living organisms, for example, they play a role in muscle contraction but also our visual perception is based on the dynamics of a molecular switch in the eye. Scientists are working intensively to develop novel molecular components that enable switching between different states, so that molecular processes can be specifically controlled.

Molecular switches are the molecular counterparts of electrical switches and play an important role in many processes in nature. Nanotechnologist now produced a photographic film at the atomic level and thus tracked the motion of a molecular building block.

Hokkaido University scientists have succeeded in synthesizing an α,α-difluoroglycine derivative, a type of α-amino acid, based on a reaction path predicted by quantum chemical calculations. This novel method, combining experimental chemistry and computational chemistry, could innovate the development of new chemical reactions.

When bacteria such as Salmonella or Yersinia cause fever, diarrhoea or abdominal pain, tiny 'injection needles' are at work: their type 3 secretion system, or T3SS for short, shoots bacterial virulence proteins directly into the eukaryotic host cells. Researchers have thought of using bacterial injection devices to introduce proteins into eukaryotic cells. A Max Planck research team has now succeeded in controlling the injection system optogenetically, i.e. with light. In the future this will enable to use the system in biotechnological or medical applications.

Neurobiologists have discovered how the signalling molecule Neuromedin U plays a crucial role in our learning process. The protein allows the brain to recall negative memories and, as such, learn from the past.

Scientists from UC San Diego, UC Santa Cruz and Duke University synchronized their research watches to study what

Researchers have revealed how an essential protein helps to activate genomic DNA during the conversion of regular adult human cells into stem cells.

A new study of molecular interactions central to the functioning of biological clocks explains how certain mutations can shorten clock timing, making some people extreme 'morning larks' because their internal clocks operate on a 20-hour cycle instead of being synchronized with the 24-hour cycle of day and night. Researchers found that the same molecular switch mechanism affected by these mutations is at work in animals ranging from fruit flies to people.

The molecular blueprint of life is stored in DNA within the genome. The digital revolution in biology, driven by DNA sequencing, enables scientists to read the genomes of the many microbes and multicellular organisms that populate our world. Today, DNA sequences of over 200,000 microbial genomes are deposited in digital genome databases and have exponentially increased the understanding of how DNA programs living systems. Using this incredible treasure trove of molecular building blocks, bioengineers learn to sequence and synthesize long DNA molecules and to breed useful microbes with the help of computers.

Researchers from the group of Vlad Cojocaru together with colleagues the Max Planck Institute in Münster (Germany) have revealed how an essential protein helps to activate genomic DNA during the conversion of regular adult human cells into stem cells. Their findings are published in the Biophysical Journal.

Chronic inflammation, which results when old age, stress or environmental toxins keep the body’s immune system in overdrive,

Scientists have identified a molecular 'switch' that controls the immune machinery responsible for chronic inflammation in the body. The finding could lead to new ways to halt or even reverse many age-related conditions, from from Alzheimer's and Parkinson's to diabetes and cancer.

A molecular switch has the ability to turn on a substance in animals that repairs neurological damage in disorders such as multiple sclerosis (MS) researchers discovered. The early research in animal models could advance an already approved Food and Drug Administration therapy and also could lead to new strategies for treating diseases of the central nervous system.

A research team has revealed a new mechanism which controls the causes of infection with H. pylori, triggering the development of stomach diseases. It is hoped that these findings will lead in time to new therapies.

A DNA computer consisting of strands of DNA in a test tube can calculate the square root of numbers up to 900

French researchers taking the fight to sarcopenia.

An organic material that can repeatedly change shape without breaking would have many useful applications, such as artificial muscles, pumps or as a switch. Physicists accidentally discovered a material with that property.

An organic material that can repeatedly change shape without breaking would have many useful applications, such as artificial muscles, pumps or as a switch. Physicists at Radboud University accidentally discovered a material with that property. Their findings will be published in the scientific journal Nature Communications on October 8th.

Research by William Kaelin Jr., Peter Ratcliffe and Gregg Semenza led the way for applications in treating anemia, cancer and other diseases -- Read more on ScientificAmerican.com

Research by William Kaelin Jr., Peter Ratcliffe and Gregg Semenza led the way for applications in treating anemia, cancer and other diseases -- Read more on ScientificAmerican.com

Circuits of chemicals could carry out calculations

Tumors and certain viral infections pose a challenge to the human body which the immune system typically fails to hand. In these diseases it switches to hypofunctional state that prevent adequate protection. A research team has achieved a major success: They identified the crucial molecular switch that triggers such dysfunctional immune responses. This could make it possible in the future to switch off or to prevent this state.

Scientists have developed an entirely new class of molecular photoswitches that meet many of the 'holy grail' requirements so far thought to be impossible to achieve.

A collaborative of institutions including the University of Groningen has developed an entirely new class of molecular photoswitches that meet many requirements previously considered unobtainable. The results have been published in Nature Communications on 3 June.

A large number of genes have to be switched on or off at different times during development. A

Computer scientists have created DNA molecules that can self-assemble into patterns essentially by running their own program.

In a paper published in the journal Circulation Research, they used this technique to uncover the effects of genetic

DNA sequencing of microbial samples can give researchers and medical professionals a wealth of information about microbiomes – the communities of microorganisms that inhabit our bodies and the environments all around us. Understanding the microbiome can aid our understanding of what ails us and why. But what happens when microbial samples are contaminated with DNA from other sources?

Researchers at MIT and Arizona State University have designed a computer program that allows users to translate any free-form drawing into a two-dimensional, nanoscale structure made of DNA.

A new quantum algorithm has been implemented for quantum chemical calculations such as Full-CI on quantum computers without exponential/combinatorial explosion, giving exact solutions of Schroedinger Equations for atoms and molecules, for the first time.

Researchers have made an unexpected and vital contribution to an international collaborative effort in Parkinson's disease research.

How to create nanocages, i.e., robust and stable objects with regular voids and tunable properties? Short segments of DNA molecules are perfect candidates for the controllable design of novel complex structures. Physicists investigated methodologies to synthesize DNA-based dendrimers in the lab and to predict their behavior using detailed computer simulations.

How to create nanocages, i.e., robust and stable objects with regular voids and tunable properties? Short segments of DNA molecules are perfect candidates for the controllable design of novel complex structures. Physicists from the University of Vienna, the Technical University of Vienna, the Jülich Research Center in Germany and Cornell University in the U.S.A., investigated methodologies to synthesize DNA-based dendrimers in the lab and to predict their behavior using detailed computer simulations. Their results are published in Nanoscale.