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Showing posts with label molecules. Show all posts
Showing posts with label molecules. Show all posts

Tuesday, 21 March 2017

Why water splashes: New theory reveals secrets

New research from the University of Warwick generates fresh insight into how a raindrop or spilt coffee splashes.

Dr James Sprittles from the Mathematics Institute has created a new theory to explain exactly what happens - in the tiny space between a drop of water and a surface - to cause a splash.

Water splash

When a drop of water falls, it is prevented from spreading smoothly across a surface by a microscopically thin layer of air that it can't push aside - so instead of wetting the surface, parts of the liquid fly off, and a splash is generated.

A layer of air 1 micron in size - fifty times smaller than the width of a human hair - can obstruct a 1mm drop of water which is one thousand times larger.

This is comparable to a 1cm layer of air stopping a tsunami wave spreading across a beach.

Dr Sprittles has established exactly what happens to this miniscule layer of air during the super-fast action by developing a new theory, capturing its microscopic dynamics - factoring in different physical conditions, such as liquid viscosity and air pressure, to predict whether splashes will occur or not.

The lower the air pressure, the easier the air can escape from the squashed layer - giving less resistance to the water drop - enabling the suppression of splashes. This is why drops are less likely to splash at the top of mountains, where the air pressure is reduced.

Understanding the conditions that cause splashing enables researchers to find out how to prevent it - leading to potential breakthroughs in various fields.

In 3D printing, liquid drops can form the building blocks of tailor-made products such as hearing aids; stopping splashing is key to making products of the desired quality.

Splashes are also a crucial part of forensic science - whether blood drops have splashed or not provides insight into where they came from, which can be vital information in a criminal investigation.

Dr Sprittles comments:

"You would never expect a seemingly simple everyday event to exhibit such complexity. The air layer's width is so small that it is similar to the distance air molecules travel between collisions, so that traditional models are inaccurate and a microscopic theory is required.

"Most promisingly, the new theory should have applications to a wide range of related phenomena, such as in climate science - to understand how water drops collide during the formation of clouds or to estimate the quantity of gas being dragged into our oceans by rainfall."

The research, 'Kinetic Effects in Dynamic Wetting', is published in Physical Review Letters.

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Tuesday, 17 January 2017

Simple fats, amino acids to explain how life began

Life is a process that originated 3.5 billion years ago. It emerged when the basic components of the cells that we know today, in other words, inanimate chemical molecules, gradually joined, merged, assembled themselves and interacted. At a given moment they became alive, or what amounts to the same thing, they turned into autonomous systems. As the years passed they gradually evolved until achieving their current complexity and diversity. A piece of research by the UPV/EHU is working on the start of this trajectory by studying how the chemical molecules assembled themselves so that life could begin.

A section of DNA. Zephyris at the English language Wikipedia [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/)], via Wikimedia Commons
DNA, RNA, proteins, membranes, sugars, …cells are made up of all kinds of components. In biology, and in the studies dealing with the origin of life specifically, it is very common to focus on one of these molecules and put forward hypotheses on how life originated by analysing the specific mechanisms related to it. "Basically, these studies are looking for the 'molecule of life', in other words, they set out to establish which was the most important molecule in making this milestone happen," said Kepa Ruiz-Mirazo, researcher in the Biophysics Unit and of the UPV/EHU's Department of Logic and Philosophy of Science. However, bearing in mind that "life involves activity among a huge variety of molecules and components, a change of approach has been taking place in recent years and research that takes into account various molecules at the same time is gaining strength," he added.

Besides emerging in favour of this fresh approach, Ruiz-Mirazo's group, in collaboration with the University of Montpellier, through an internship of the UPV/EHU PhD student Sara Murillo-Sánchez, has been able to show that interaction exists between some molecules and others. "Our group has expertise in research into membranes that are created in prebiotic environments, in other words, in the study of the dynamics that fatty acids, the precursors of current lipids, may have had. 

The Montpellier group for its part specialises in the synthesis of the first peptides. So when the knowledge of each group is put together, and when we experimentally blended the fatty acids and the amino acids, we could see that there was a strong synergy between them."

As they were able to see, the catalysis of the reaction took place when the fatty acids formed compartments. As they are in an aqueous medium, and due to the hydrophobic nature of lipids, they tend to join with each other and form closed compartments; in other words, they take on the function of a membrane; "at that time the membranes obviously weren't biological but chemical ones," explained Ruiz-Mirazo. In their experiments they were able to see that the conditions offered by these membranes are favourable for amino acids. "The Montpellier group had the prebiotic reactions of the formation of dipeptides very well characterised, so they were able to see that this reaction took place more efficiently in the presence of fatty acids," he added.

Besides demonstrating the synergy between fatty acids and amino acids, Ruiz-Mirazo believes it is very important to have conducted the study using basic chemical components, in other words, molecular precursors. "Life emerged out of these basic molecules; therefore, to study its origin we cannot start from the complex phospholipids that are found in today's membranes. We have demonstrated the formation of the first coming together and formation of chains on the basis of molecular precursors. Or to put it another way, we have demonstrated that it is possible to achieve diversity and complexity in biology by starting from chemistry."

In his studies, in addition to the experimental work, Ruiz-Mirazo is working in another two spheres so in the end he is studying the origin of life from three pillars or perspectives: "firstly, we have the experimental field; another is based on theoretical models and computational simulations, which we use to analyse the results obtained in the experiments, and the third is a little broader, because we are studying from the philosophical viewpoint what life is, the influence that the conception held about life exerts on the experimental field, since each conception leads you to carry out a specific type of experiment," he explained. "These three methodologies mutually feed each other: an idea that may emerge in the philosophical analysis leads you to carry out a new simulation, and the results of the simulations mark out the path for designing the experiments. Or the other way round. Most likely we will never manage to find the answer to how life began, but we are working on it: all of us living beings on Earth have the same origin and we want to know how it happened."

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Tuesday, 15 November 2016

What molecules you leave on your phone reveal about your lifestyle

We leave behind trace chemicals, molecules and microbes on every object we touch. By sampling the molecules on cell phones, researchers at University of California San Diego School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences were able to construct lifestyle sketches for each phone's owner, including diet, preferred hygiene products, health status and locations visited. This proof-of-concept study, published November 14 by Proceedings of the National Academy of Sciences, could have a number of applications, including criminal profiling, airport screening, medication adherence monitoring, clinical trial participant stratification and environmental exposure studies.

"You can imagine a scenario where a crime scene investigator comes across a personal object - like a phone, pen or key - without fingerprints or DNA, or with prints or DNA not found in the database. They would have nothing to go on to determine who that belongs to," said senior author Pieter Dorrestein, PhD, professor in UC San Diego School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences. "So we thought - what if we take advantage of left-behind skin chemistry to tell us what kind of lifestyle this person has?"

Mobile phone evolution. By Anders (Own work) , via Wikimedia Commons

In a 2015 study, Dorrestein's team constructed 3D models to illustrate the molecules and microbes found at hundreds of locations on the bodies of two healthy adult volunteers. Despite a three-day moratorium on personal hygiene products before the samples were collected, the researchers were surprised to find that the most abundant molecular features in the skin swabs still came from hygiene and beauty products, such as sunscreen.

"All of these chemical traces on our bodies can transfer to objects," Dorrestein said. "So we realized we could probably come up with a profile of a person's lifestyle based on chemistries we can detect on objects they frequently use."

Thirty-nine healthy adult volunteers participated in Dorrestein's latest study. The team swabbed four spots on each person's cell phone - an object we tend to spend a lot of time touching - and eight spots on each person's right hand, for a total of nearly 500 samples. Then they used a technique called mass spectrometry to detect molecules from the samples. They identified as many molecules as possible by comparing them to reference structures in the GNPS database, a crowdsourced mass spectrometry knowledge repository and annotation website developed by Dorrestein and co-author Nuno Bandeira, PhD, associate professor at the Jacobs School of Engineering and Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego.

With this information, the researchers developed a personalized lifestyle "read-out" from each phone. Some of the medications they detected on phones included anti-inflammatory and anti-fungal skin creams, hair loss treatments, anti-depressants and eye drops. Food molecules included citrus, caffeine, herbs and spices. Sunscreen ingredients and DEET mosquito repellant were detected on phones even months after they had last been used by the phone owners, suggesting these objects can provide long-term composite lifestyle sketches.

"By analyzing the molecules they've left behind on their phones, we could tell if a person is likely female, uses high-end cosmetics, dyes her hair, drinks coffee, prefers beer over wine, likes spicy food, is being treated for depression, wears sunscreen and bug spray - and therefore likely spends a lot of time outdoors - all kinds of things," said first author Amina Bouslimani, PhD, an assistant project scientist in Dorrestein's lab. "This is the kind of information that could help an investigator narrow down the search for an object's owner."

There are limitations, Dorrestein said. First of all, these molecular read-outs provide a general profile of person's lifestyle, but they are not meant to be a one-to-one match, like a fingerprint. To develop more precise profiles and for this method to be more useful, he said more molecules are needed in the reference database, particularly for the most common foods people eat, clothing materials, carpets, wall paints and anything else people come into contact with. He'd like to see a trace molecule database on the scale of the fingerprint database, but it's a large-scale effort that no single lab will be able to do alone.

Moving forward, Dorrestein and Bouslimani have already begun extending their study with an additional 80 people and samples from other personal objects, such as wallets and keys. They also hope to soon begin gathering another layer of information from each sample - identities of the many bacteria and other microbes that cover our skin and objects. In a 2010 study, their collaborator and co-author, Rob Knight, PhD, professor in the UC San Diego School of Medicine and Jacobs School of Engineering and director of the Center for Microbiome Innovation at UC San Diego, contributed to a study in which his team found they could usually match a computer keyboard to its owner just based on the unique populations of microbes the person left on it. At that time, they could make the match with a fair amount of accuracy, though not yet precisely enough for use in an investigation.

Beyond forensics, Dorrestein and Bouslimani imagine trace molecular read-outs could also be used in medical and environmental studies. For example, perhaps one day physicians could assess how well a patient is sticking with a medication regimen by monitoring metabolites on his or her skin. Similarly, patients participating in a clinical trial could be divided into subgroups based on how they metabolize the medication under investigation, as revealed by skin metabolites - then the medication could be given only to those patients who can metabolize it appropriately. Skin molecule read-outs might also provide useful information about a person's exposure to environmental pollutants and chemical hazards, such as in a high-risk workplace or a community living near a potential pollution source.

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Tuesday, 8 March 2016

Celebrating women in science on International Women’s Day: Dorothy Mary Hodgkin

Dorothy Mary Hodgkin OM FRS (12 May 1910 – 29 July 1994), known professionally as Dorothy Crowfoot Hodgkin or simply Dorothy Hodgkin, was a British biochemist who developed protein crystallography, for which she won the Nobel Prize in Chemistry in 1964.

She advanced the technique of X-ray crystallography, a method used to determine the three-dimensional structures of biomolecules. Among her most influential discoveries are the confirmation of the structure of penicillin that Ernst Boris Chain and Edward Abraham had previously surmised, demonstrating (contrary to scientific opinion at the time) that it contains a β-lactam ring. She also confirmed the structure of vitamin B12, for which she became the third woman to win the Nobel Prize in Chemistry.  In 1945, working with C. H. (Harry) Carlisle, she published the first such structure of a steroid, cholesteryl iodide (having worked with cholesteryls since the days of her doctoral studies). 

In 1948, Hodgkin first encountered vitamin B12 and created new crystals. Vitamin B12 had first been discovered by Merck earlier that year. Vitamin B12 had a structure at the time that was almost completely unknown, and when Hodgkin discovered it contained cobalt, she realized the structure actualization may be determined by x-ray crystallography analysis. The large size of the molecule, and that the atoms were largely unaccounted for - aside from cobalt - posed a challenge in structure analysis that hadn't been previously explored.

Molecular structure of vitamin B12, by NEUROtiker (Own work) [Public domain], via Wikimedia Commons

From these crystals, she deduced the presence of a ring structure because the crystals were pleochroic, a finding which she later confirmed using X-ray crystallography. The B12 study published by Hodgkin was described by Lawrence Bragg as being as significant "as breaking the sound barrier." Scientists from Merck had previously crystallised B12, but had published only refractive indices of the substance. The final structure of B12, for which Hodgkin was later awarded the Nobel Prize, was published in 1955.

In 1969, after 35 years of work and five years after winning the Nobel Prize, Hodgkin was able to decipher the structure of insulin. X-ray crystallography became a widely used tool and was critical in later determining the structures of many biological molecules where knowledge of structure is critical to an understanding of function. She is regarded as one of the pioneer scientists in the field of X-ray crystallography studies of biomolecules.

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Friday, 15 August 2014

What is Brownian Motion?

The term 'Brownian motion' (or 'Brownian movement') refers to the apparently random, haphazard movement of microscopic particles which are suspended in a fluid - (a liquid or a gas) resulting from their collision with the quick atoms or molecules in the gas or liquid.

This is a simulation of the Brownian motion of a big particle (dust particle) that collides with a large set of smaller particles (molecules of a gas) which move with different velocities in different random directions.
Although a number of earlier workers had observed this phenomenon, it was first described, and therefore named after, the British botanist, Robert Brown, who was studying pollen grains in 1827. Brown was an accomplished microscopist. It was he who, for example, first identified the naked ovule in the gymnospermae; this is a difficult observation to make even with a modern instrument.

Brown was attempting to further his work on the mechanisms of fertilisation in flowering plants and was looking at pollen.  He believed that he would be able to examine the pollen grains more effectively through his microscope if they were suspended in water, a technique known as 'water-immersion'. To his annoyance, he observed that the pollen grains danced continuously and erratically around in the water, thus interfering with his observations. From these observations he satisfied himself that the movement:

'arose neither from currents in the fluid, nor from its gradual evaporation, but belonged to the particle itself'.

Decades later, Albert Einstein published a paper in 1905 that explained in precise detail how the motion that Brown had observed was a result of the pollen being moved by individual water molecules.

Despite all of this knowledge, scientists continue to be fascinated by the origin and nature of Brownian motion, which is still imperfectly understood. Articles concerning the mathematics of Brownian motion continue to be published in contemporary physics journals.

For more information visit:-
http://en.wikipedia.org/wiki/Brownian_motion