Questions tagged [biophysics]

The use of methods from the physical sciences to aid in the study of biological systems.

44 questions with no upvoted or accepted answers
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122 views

How to measure Na/K channel activation at the membrane level?

Assume that there are two different signals occurring on the ECG - during depolarization and repolarization in the standard ECG. I was advised not to use the standard ECG in measuring the exact ...
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173 views

Protein phosphorylation in the cytoplasm. Typical time scale?

Is there a typical protein phosphorylation rate in the cell cytoplasm under physiological conditions, or at least an upper-bound? Suppose a protein $A$ is being phosphorylated into $A^*$ with the ...
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58 views

What are necessary parameters for a tissue scaffold to be biodegradable?`

I am a mechanical engineer with little biological experience, but I have recently been looking at tissue scaffoldings. My current understanding is as follows, but may be flawed. I would appreciate ...
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84 views

Photosynthetic efficiency and light harvesting efficiency

Is there some sort of measure of the light harvesting efficiency (possibly like transfer time) that is directly related to the photosynthetic efficiency in some sort of equation? Also, how important ...
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63 views

What structures (i.e. organs) are suspended by tensile forces?

In several areas of biomechanical literature I have read, the concept of "tensegrity" has arisen. Definitions are as follows: “The integrity of a stable structure balanced by continuous structural ...
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172 views

Is it possible to biologically convert potential energy to chemical energy?

To lift an object x meters it is necessary to expend, at a minimum, an amount of energy corresponding to the increase in that objects potential energy associated with the increase in height. When ...
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54 views

Infrared emitting diode eye safety

I'm thinking of creating my own laser tag system and am a bit concerned about the eye safety aspect. Most of the homebrew system I've seen use the TSAL 6100 diode(http://www.vishay.com/docs/81009/...
3
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87 views

How to get a pdb file of a single atom?

I am trying to get a pdb file that contains a single atom, it doesn't matter if it's Hydrogen or another atom. How can I obtain this? Are there any pdb files with just a single atom available to ...
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56 views

What is the charge of (bacterial) ribosome?

Ribosomes are negatively charged and thus electrostaticaly repelled from DNA. However, I could not find a good reference that would allow me to estimate the magnitude of negative charge on a ribosome. ...
2
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27 views

How does nitrogen gas partial pressure change when ascending during scuba dive?

Scuba divers suffer decompression illness in which during sudden ascension, gas bubbles form in blood vessels and do not get reabsorbed quickly, leading to various problems including a stroke. The ...
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139 views

What is the biological relevance of RIPPLE phase in membranes?

I was reading about ripple phase in bilayer lipid membranes which is described here as a meta-stable state between lamellar tilted crystalline and lamellar fluid state. It is also known that ripple ...
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36 views

Validity of Acoustic Weapon Effects on Biological Organisms?

There is alot of rather contradictory information present on the biological effects of acoustic weapons with a bevy of scientific articles claiming that they cause harm to biological organisms with ...
2
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49 views

Are trees still carrying their leaves more likely to be felled by an autumn storm?

Is there evidence that trees still carrying their leaves are more likely to be felled by an autumn storm than trees already having lost their leaves? At first sight this seems plausible (and might be ...
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114 views

Membrane resistance of a neuron

I am about to simulate a neuron activity with the "Leaky Integrate and Fire" neuron model. But for that I need the membrane resistance. I was really looking a lot online, but I just cant find a value. ...
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40 views

How to use the law of diffusion in the presence of electric forces?

Isn't the movement of ions affected by the electric field as well? For instance, when a sodium channel in a cell's membrane opens, the sodium ions are said to diffuse into the cell, from higher ...
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36 views

Interaction study of oligomeric proteins

I'm dealing with two different protein(say, protein_a and protein_b) which stays in an interacting-oligomeric form in biological system. I have so far successfully been able to purify both the ...
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157 views

How spermaceti makes a whale float

In the biochemistry book I'm reading (Box 10-1, Lehninger Principles of Biochemistry), an example is given in whales of how spermaceti (a wax located in the whale head), when at sea level is a liquid, ...
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1k views

How can the directionality of a protein structure be defined?

For a DNA molecule, you can define directionality using the convention of a 5'-3' direction on the Sense strand. However, using an N to C convention for a protein doesn't work since the ends may be on ...
2
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1answer
778 views

Can a mathematical function be assigned to ECG diagram?

This is a 12 lead electeocardiogram of a 26 year old male: This is the graph of function $5sin(7x)sin(.5x)cos(3.25x)$ This graph look quite similar to the ECG diagram.After sketching this graph, I ...
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47 views

Can enzymes be modeled using classical mechanics?

When enzymes interact with substrates (i.e. a small ADP molecule and the much larger ATP synthase), does quantum mechanics play a significant role? Or can the interactions be relatively accurately be ...
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51 views

Bioenergetics book

I already asked this question on the physics SE but redirected here: In the field of biophysics, it seems there is a subfield called "bioenergetics" about the processes of generating energy by ...
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19 views

What is the native structure of amyloid-beta protein under physiological conditions?

The amyloid-beta protein forms cross-beta structured fibrils. But under normal physiological conditions what is their predominant secondary structure. Is it alpha-helix, random coil or beta-sheet?
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84 views

What waste products do cells secrete in culture, and at what rate?

I am designing microfluidic chips for mammalian cell culture. One aspect I am interested in modeling is the rate at which I must renew media to ensure that: Cells receive enough nutrients Cytotoxic ...
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50 views

effect of arterial vasocontriction on the pressure in arteries

if experimentally one induces smooth muscle contraction on an artery and cause it to constrict, keeping the cardiac output same and also the arteriolar resistance(total peripheral resistance) the same ...
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98 views

law of laplace and pressure developed in arteries

in arterioles the pressure depends on the impedance of the vessel(elasticity and youngs modulus) cardiac output pre arteriolar resistance what i want to ask is will the pressure also depend on law of ...
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36 views

Calcium and nitric oxide: does a numerical relationship exist?

Currently, I am trying to understand how nitric oxide and calcium are related during the production of the former (I am not a biologist nor a chemist, so my knowledge about these topics is very poor). ...
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39 views

Will charged water ions sprayed onto plants keep insects off?

I had stumbled on an article about a Dutch firm that devised an irrigation system that used mist of ionized water droplets that they claim keeps insects away from the plants. This break through would ...
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39 views

Why do nerve fibres rotate?

Background: Lemniscus (Latin lēmniscus, ribbon) is a strap of second order nerve fibres which twist as they ascend to the brainstem. Why do these these nerve fibres rotate? What could be the ...
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42 views

What will CD spectroscopy show when L- and D- forms of proteins are mixed?

What will happen if equimolar concentration of L- and D- forms of proteins are mixed and we take the circular dichroism reading? Will the positive and negative ellipticity cancel each other out or ...
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123 views

GFP brightness calculation

So this question is part math, part biology, but I'm asking about the biology part here (or maybe the chemistry part). Basically I'm asking about my attempt to calculate the possible brightness per ...
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70 views

How much Cardiomyocyte Move in Relation to its Neurons?

I am trying to estimate how much cardiomyocyte and its things (mitochondria) move in relation to neurons Movement of neurons (1) Movement of cardiomyocytes Movement of cardiomyocytes' mitochondrias (...
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41 views

Natural rulers: What organisms have the most regular size?

What organisms exhibit the most precise length scales? E.g. are there trees with rings that are of very precise thickness, or single celled organisms which are all very nearly the same length? In ...
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34 views

Phase Transitions of Purified Proteins

Why do solutions of purified protein condense into droplet phases? I'm trying to understand the protein phase transitions. Here is the article http://www.cell.com/cell/fulltext/S0092-8674(12)00634-4#...
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77 views

Why do the vines change their spinning direction?

Look at the vines holding onto the lattice. The "vine springs" change their spinning direction in the middle. Why? And how do they achieve this? (By the way, what's the name for this plant? Is is ...
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97 views

Absorbed dose from a CT scan with relation to radiation accidents

I read somewhere that the average CTDIvol in CT scans at hospitals is ~40 mGy. This translates to the 'radiation intensity' at the center of the person, and can also be roughly interpreted as an '...
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293 views

What is the sedimentation coefficient of Mycoplasma?

I have attempted to find the sedimentation coefficient of a number of bacterial species, namely E. coli and a number of Mycoplasma species, but they seemed to be rather elusive in the literature. If ...
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147 views

Meaning of 'forms of free energy'?

I was doing a practice exam paper and it asked for different 'forms of free energy'. I am a physicist rather then a biologist so 'free energy' to me means Gibb's Free Energy: $$G=H-TS$$ But I cannot ...
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20 views

How to include multiple DNAs into a crystal structure

I have a crystal structure (PDB 3OS1)that shows the interaction of PFV intasome with a substate DNA. I would like to replace the existing DNA in the intasome as well in the substrate with a longer ...
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24 views

“Straight” or “linear” helix

If an alpha helix is discontinued for a short while and then continues in a different direction, I prefer to call in "kinked". If the helix is simply uniformly following one direction, I prefer to ...
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13 views

What are the methods to measure the surface density of animals in biology?

In biology there is a rule found by Damuth (https://www.nature.com/articles/290699a0): a relationship between the size of an animal species $l$ and its local abundance (surface density) $N/S$ $$N/S=...
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13 views

Time span until everything biological is stabilized/finalized after a low-level exposure to ionizing radiation?

Say the x-rays of a common diagnostic CT (< = 10 mSv?). Irrespective of any ultimate effects (linear or threshold detrimental, inconsequential, or even protectively hormetic) just how long until ...
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44 views

How to derive the deactivation time constant in this model of Acetylcholine Receptor state kinetics?

I came across this simple analytical expression of time constant of deactivation in Elenes et al., 2006. How does one derive this expression $$\displaystyle\tau_\text{deactivation}\approx\frac{1}{D_+ ...
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21 views

Using Diffusion Constant to calculate time taken to travel

Is there a way to use D , the diffusion constant to estimate the time taken to travel across a cell. E.g one of 100 micro metres. Or by the very random nature of brownian motion is this impossible?
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1answer
29 views

Square-cubed law and health

Does the square-cubed law lead to possible health detriments for taller people? I'm not sure what the optimum height is for humans (e.g. due to their cross-sectional bone density constraints), but ...