USP Laser Shatters Capsids — Update

Posted January 7, 2008 by Hip
Categories: Blogroll

The ultra-short pulse laser antiviral research by Tsen & Tsen, discussed in the previous post, is gathering momentum. Already, two physicists at Arizona State University, Eric Dykeman and Otto Sankey, are modeling capsid vibrations, hoping that their theorectical calculations of capsid resonance will coincide with the resonance frequencies measured experimentally by KT Tsen at Arizona.

So far, Dykeman and Sankey’s model (currently based on the tobacco necrosis virus) predicts a capsid resonance frequency in the region of 60 to 90 GHz.

If capsid resonant frequencies can be determined for all viruses, there is a possibility that light pulses at the precise GHz rate can be used to shatter and destroy any virus, much in the same way that an opera singer can shatter glass if their voice is pitched exactly at the resonance vibration frequency of the glass.

Further Info

Ultrashort-Pulse Laser Shatters Viruses

Posted November 8, 2007 by Hip
Categories: Biotechnology, Blogroll, Health, Immunology, Medicine, Microbiology, Science, Technology, virology

A father and Son team have devised a revolutionary laser method that disintegrates viruses without damaging surrounding cells.

Johns Hopkins University student Shaw-Wei David Tsen was looking for a new way to rid isolated blood of pathogens such as the HIV and hepatitis C viruses. Current virucidal methods based on ultraviolet irradiation often damage blood components.

With his father, physicist and laser expert Kong-Thon Tsen, they developed a technique using ultrashort-pulse lasers to create a forced resonance in the virus shell. The laser pulse mechanically vibrates the capsid shell of a virus, which then shatters it, leaving behind a harmless debris of just component molecules. Ultrashort-pulse lasers (USPs) do not generate much heat, and tests have already shown that viral capsid shells will disintegrate at energies far lower than that which would harm adjacent cells.

They first considered using ultrasound resonance, but Kong-Thon Tsen, a laser expert at Arizon State University realized that lasers are better at penetrating the energy-absorbing water surrounding the virus particles. This revolutionary new method should be effective in destroying a wide range of viruses and bacteria.

When tested on bacteriophage viruses, the quantity of infectious virions decreased by as mush as 1000-fold after laser treatment. They are now testing the system on HIV and Hepatitis C virions.

The laser induces a dipole moment in the virus’s capsid, which creates a force within the virus, so that the virion becomes unstable and breaks apart.

References:
Photonics, WIRED, John Hopkins, Laser Focus World Article
Forced Resonance Ultra-Short Pulse Laser Kills Viruses Dead
Original paper, Journal of Physics: Condensed Matter, Nov 2007
Also, checkout Raydiance, a company that offers self-contained, software-controlled ultra-short pulse laser equipment that can fit in a suitcase (previously they needed the space of an entire physics laboratory). These smaller ultra-short pulse lasers are set to revolutionize medicine.

The Ultimate Virucide – Chiral Humans

Posted September 21, 2007 by Hip
Categories: Biotechnology, Blogroll, Health, Immunology, Medicine, Microbiology, Science, Technology, virology

Immunity by Incompatibility

Arthur C. Clarke writes about a molecular mirror-image human being starving to death because his body cannot process normal sugars (see “Technical Error” in his book The Collected Stories).

Jarek Duda takes this idea further, and shows us how we can prevent virtually ANY microbe (virus, bacterium, fungus, protozoan, etc) from infecting us – by constructing mirror-image (chiral) human beings which will be totally incompatible to these microbes!

Reconstructing ourselves in chiral form, using the mirror-image reflection of our cellular components is achieved by replacing left-handed amino acids with right-handed ones, in order to create mirror reflections of all human proteins. Analogically, we could get chiral sugars, DNA, etc, on which reflected enzymes would work perfectly. Finally we would get a normally functioning molecular mirror reflection of a natural organism – a chiral counterpart organism – with which natural viruses and bacteria couldn’t interact. Electromagnetic force (chemistry) is unchanged under such molecular reflection transformation (P-symmetry). There is a small alteration of weak interactions under reflection, which can produce very small corrections, but these corrections are many orders of magnitude lower than thermal noise – almost certainly too tiny to alter any biochemistry.

Life on Earth only uses left-handed amino acids. All of biology has this homochirality. Chiral (right-handed) amino acids do not exist in nature, so any such chiral organism would be entering completely virgin territory, biologically speaking.

Such a chiral organism would obviously need to be feed with chiral food, produced by chiral plants. The great advantage, though, is that such chiral organisms would enjoy a disease-free life, completely immune to all viruses and microbes. And we would eliminate plagues and epidemics.

Viruses would be completely incompatible with the reflected human cellular structures; and bacteria, protozoa and fungi could not function because they would not be able to find normal sugars inside reflected organisms. The reverse sugars circulating in the chiral human body would be indigestible as far as normal bacteria are concerned, so any bacterium entering a chiral human would simply starve to death. The chiral environment is absolutely hostile for normal viruses, protozoa, bacteria, etc.

In order to infect a chiral human, existing bacteria would have to evolve their own mirror image structure from scratch. This is extremely unlikely to happen (since DNA holds the genes, the alphabet of evolution, but DNA itself is a priori to genes, and therefore more or less untouched by the process of evolution). Terrorist acts, however, are a concern. In the case of sabotage, we would have to control the spread of any terrorist-engineered chiral virus using the anti-terrorist and anti-biowarfare measures that we already have in place today.

How do we create a chiral organism, such as a reflected human? The synthesis of every molecule, a reflected zygote is difficult, because we don’t have chiral enzymes. But the real problem is creating the correct structure of membranes with specific concentrations. Nevertheless, with advancing nano-engineering, this could be possible in say 50 years, when we could slowly transform our ecosystems, starting from the bacterium E. coli, which will act as our factory, and later plants. Finally, if all goes well, the human being.

But in such a sterile environment, would we have perfect health? Perhaps the stresses created by small infections can, like small amounts of radiation, have positive long-term influence? For example, infection helps to get rid of damaged and weak cells in an organism. And the hygiene hypothesis states that the actual absence of exposure to microbes can lead to autoimmune diseases (although more probably, autoimmune diseases are due to chronic underlying infection from viruses and bacteria that have insinuated themselves deeply inside a living organism and its cells, rather than the lack of exposure to microbes; so we might in this way eliminate autoimmune conditions as well once humans move into chiral life).

We would also need to be careful about human endogenous retroviruses (HERVs). These are virus gene coding sequences that exist within the human genome (they originate from ancient infections), which theoretically can come to life as a virus. HERVs are best eliminated from our genome before we switch to chiral form, otherwise if these ancient viruses come to life in chiral form, they could evolve and mutate into new retroviruses viruses that could infect chiral human being society. We want create chiral life completely and totally free of chiral viruses, or any other chiral microorganism.

There are other dangers too: imagine a reflected unicellular organism, which needs only light and symmetric molecules like H2O, CO2, O2. Such a chiral unicellular organism could spread, evolve, and could even overthrow plant life.

So the main rule from the beginning should be: in the case of chlorophyll organisms: only plants whose population can be controlled should be transformed!

Transformation of our ecosystem would be expensive, but in the future we may need to create completely new ecosystems for populating other planets like Mars. In these situations, the effectiveness of such an ecosystem will be very important. We would need many kinds of microorganisms. Symbiotic ones wouldn’t need to have aggressive mechanisms; aggressive microbes would only re-emerge if they evolved from zero. I cannot imagine that chiral viruses would be needed; they wouldn’t be transformed at all. Thus chiral viruses would just re-appear if they evolved from zero, like free DNA, which isunlikely. Furthermore, the last time this happened, the viruses evolved in parallel with their targets; now organisms have very advanced specific and non-specific defensive systems, which will make it hard for any chiral virus to appear and establish itself in a chiral ecosystem.

Of course, once our ecosystem is transformed, if in the distant future, we find a new major problem, we can always reverse again!

Another option, which is much easier, is to  just switch humans to chiral form, leaving the rest of the ecosystem untouched. In the near future, it is likely that we will bio-engineer some of our food, so we could just bio-engineer our own factory-made chiral foods, without needing to introduce chiral plants for our crops, or chiral animals for our meat.

This chiral humans-only approach would be much easier and safer than converting the whole ecosystem to chiral form, and we could then enjoy all of nature in its pure and natural form, without ever having to worry about parasites or infections, which we will have jumped beyond forever.

ADD YOUR COMMENTS.

Further discussion and comments can be found here: SCIENCE FORUMS, GREG BEAR.

If You Can’t Beat Them, Join Them

Posted February 28, 2007 by Hip
Categories: Biotechnology, Blogroll, Health, Immunology, Medicine, Microbiology, Science, Technology, virology

I recently came across this clever antiviral idea which utilises short RNA molecules to usurp the replication machinery in a virus infected cell. This concept was devised by John Yin and Hwijin Kim at the University of Wisconsin-Madison. So, rather than trying to destroy viruses inside an infected cell, instead you simply take over the cellular machinery that the virus uses to replicate, to prevent viral proliferation. In a computer simulation, as these RNA molecules are introduced into the cell, they themselves begin to replicate, taking over of the cell’s resources, lowering of the rate of virion reproduction from 500 per minute, down to zero.

A nice concept.

It makes one question whether the cell’s replication machinery can be controlled in this way, using other means, such as radiowave interference. Some recent research has shown that FM radio waves (100 MHz) are a strong causal factor in melanoma. The hypothesis is that FM waves may be interfering with the cell’s natural DNA repair mechanism, apoptosis mechanism, and/or the body’s immune system. Thus if FM radio frequencies can do this, we may be able to find a radio frequency that can slow down the replication process in cells, and lower viral replication rates to zero.

ADD YOUR COMMENTS

Infrared Light In Vivo

Posted February 21, 2007 by Hip
Categories: Blogroll

NASA have carefully researched the effect of infrared and visible-light electromagnetic radiation on body metabolism. Though their research relates to wound healing, bone density and cell growth (rather than our antiviral objectives), it usefully demonstrates the biologically active effect that specific infrared and visible-light wavelengths have on the body. This is interesting data. References: 1 2 3

One infrared device that does have a demonstrable effect against viral infection is the Virulite, which operates with an LED light of wavelength 1072nm (1072nm was chosen as it represents a peak in the transmission spectrum of the water molecule). The Virulite speeds up HSV cold sore healing, although this is not via direct virucide.

ADD YOUR COMMENTS

Interaction of Radiation with Matter

Posted February 18, 2007 by Hip
Categories: Blogroll

In line with the general ethos of this site, we open our physicist’s toolbox of ideas and concepts, and examine the many ways electromagnetic radiation interacts with matter. Within this sphere of radiation–matter interaction, we hope to find a universal means of destroying any virus within the human body.

The succinct web page Interaction of Radiation with the Human Body details some of the physiological effects of the entire electromagnetic spectrum on the human body; these effects, we believe, will be the basis of our sought-after method for universal virus destruction. VIROLOGY Infrared VirucideNotice how both infrared and microwave frequencies strongly interact with the molecules in human tissue, generally resulting in heating effects from spectral absorption. One virucidal idea we examined earlier is the application of an appropriate frequency of electromagnetic radiation to tune into the spectral absorption lines of molecules within the virion, in order to selectively heat up and destroy the virions within an infected person. Such a method is described here.

The frequency and power level of our electromagnetic radiation are just two parameters we can control and adjust. Other factors we can play with include the type of electromagnetic polarization, and whether we use polychromatic or monochromatic (eg, laser) light or radiation. Monochromatic light has a very precise frequency, which may help us selectively tune into the spectral absorption lines of our target molecules in the virion, thus delivering destructive energy to them.

In addition, we may also use purely magnetic fields (eg, from a solenoid), purely electric fields (ordinary electric current or electrostaic potential), both uniform or oscillating, and at various power levels.

Furthermore, there are specialised pulsed electromagnetic fields, such as those of electroperturbation machines, which use fast nanosecond pulses to efficiently deliver sharp electrical jolts to the interior of a cell (normally, the cell interior is electrically protected by its outer membrane). References: 1 2

All in all, our physicist’s toolkit looks pretty impressive.

Additional References: Brief details on the underlying mechanisms of the various interactions of radiation and matter. A comprehensive summary of matter-radiation interactions. Electromagnetic spectrum graphics: 1 2

ADD YOUR COMMENTS

Lattice Vibration Destruction

Posted February 16, 2007 by Hip
Categories: Blogroll

For DNA viruses the pressure inside the capsid is around 60 atmospheres, and under this pressure, the viral DNA changes to crystalline form. References: 1 2

Like all crystals, crystalline DNA should have a lattice vibration absorption spectrum, and this means there will be certain frequencies of electromagnetic radiation which VIROLOGY Crystalline Virucidefacilitate maximum energy transfer when incident on the crystal. So, by applying such a frequency to a patient, we may be able to heat the all the crystalline viral DNA in his body to a sufficient degree to destroy it.

This idea depends on our electromagnetic frequency being able to penetrate into the body, otherwise we will not be able to reach all the virus particles within a patient. If the frequency is within radiowave, microwave or the terahertz range, then there is no problem, as most electromagnetic frequencies in these ranges generally penetrate human tissue.

ADD YOUR COMMENTS

Energy Absorption & Capsids

Posted February 15, 2007 by Hip
Categories: Blogroll

The Bursting the Viral Capsid post was about increasing the viral capsid’s internal pressure, thereby bursting the capsid, and destroying the virus.

This post continues with the capsid-rupture theme, but considers a different technique, based on a molecular electromagnetic energy absorption, which, as we explain below, may be able to heat-rupture viruses in the body.

VIROLOGY CapsidWe start with some preamble: note that all molecules can absorb electromagnetic energy. The degree of energy absorption depends on the frequency of the electromagnetic radiation. For a given molecule, there will be a number of electromagnetic frequencies at which that molecule strongly absorbs energy from the incident radiation. The absorbed electromagnetic energy is converted to modes of vibration and rotation of the molecule, which serve to heat the molecule and its surroundings.

Energy absorption by rotational modes requires microwave frequencies. Energy absorption by vibrational modes requires infrared frequencies.

Note: microwave rotational absorption is only possible for dipolar molecules (for example water, ammonia and ethanol molecules).

The water molecule, for example, absorbs energy at both infrared and microwave frequencies. Microwave cooking ovens make use of this. These ovens generate microwave radiation at a frequency of 2.45 GHz, which gets absorbed by all the water molecules in the food, raising the temperature and heating the food. Interestingly, 2.45 GHz is a little lower than the frequency of maximum microwave energy absorption of the water molecule; this was purposely arranged, so as to ensure that the microwaves are not all absorbed by the first layer of water they encounter in the food, and can thus penetrate deeper. Note than the microwaves do not directly heat the other molecules present in the foodstuff; the microwave frequency is specifically tuned to get absorbed by the water molecules. Microwaves will, of course, heat any conducting material placed in the oven, but this is by a completely different mechanism, that of induced electrical current (the mechanism examined in the Bursting the Viral Capsid post).

For our purposes here, we want to heat-rupture a virus in vivo, via molecular energy absorption. So we need to find a target molecule within the capsid protein wall or capsid interior that we can heat up using electromagnetic radiation with a frequency that the molecule efficiently absorbs. We will probably have to use microwaves for this, only because these easily penetrate through the human body (by contrast, infrared penetrates only a few inches of body tissue at most, and so cannot reach and treat the body’s deep interior).

We must ensure two conditions:

(1) That our target molecules exist within the virion in high concentration, but not elsewhere in the body (or only in low concentration). We want to heat the virions, not the rest of the body.

(2) That the particular frequency of radiation used to heat the target molecule does not substantially heat the other molecules (eg, water) present in the body tissues. Otherwise the electromagnetic energy will be dissipated before it reaches the target molecules in the virions.

These two conditions can be handled empirically rather than theoretically. We can expose a culture of virions to each frequency (in turn) within the microwave spectrum, and for each frequency, measure the temperature rise in the culture. The temperature rise reflects the degree of energy transfer to (unknown) target molecules within the virion for that particular frequency. We will be on the lookout for frequencies that very efficiently transfer energy from our electromagnetic radiation to the virion. Then, out of the set of efficient transfer frequencies noted, we choose the frequency that is least absorbed by other body tissues. Thus we have frequency-tuned into selectively heating (and inactivating) the virions.

With this approach, and with sufficient microwave power levels, we may be able to deliver enough heat energy to the virions, so as to increase their internal temperature and pressure, and burst the capsid. Even if we cannot raise the temperature to capsid bursting point, the heat may be sufficient to destroy the viral DNA (or RNA), which equally serves to destroy the virion.

Safety for the patient is obviously of concern. It is important to use microwave frequencies that are not significantly absorbed anywhere else in the body, apart from in viral particles. We do not want to destroy healthy tissue.

Note: this microwave method assumes there are dipolar molecules within the virion, which, as explained, are the only class of molecules that will absorb microwave radiation.

Variations on the theme: if we cannot find a dipolar target molecule naturally present within the virion that we can heat up, then there may be a way to develop a drug-based dipolar target molecule which, when taken by a patient, incorporates itself with the viral DNA, or the capsid protein wall, or penetrates into the virion, so that the virion can then be heat-destroyed by microwaves.

Note: this method may equally be applied to destroying cancer cells, provided you find a suitable dipolar target molecule inside these cells, again, not present elsewhere in the body; or develop a drug which is selectively absorbed by cancer cells, and which can then serve as the target molecule for microwave heat-destruction of these cells.

Note that the virucidal methods here are equally valid (and in some ways better suited) for destroying viruses in blood transfusion products. Though blood used for transfusion is usually screened for such viruses as HIV, it nevertheless usually contains many other viruses, which can then infect the patient during transfusion and so possibly cause health problems in the long term. Furthermore, with blood products in vitro, infrared can be used as well as microwave, as obviously infrared’s inability to deeply penetrate tissue is not a concern in this case: the blood can be infrared-treated as it flows through a narrow tube. So we have a larger spectrum, in terms of finding suitable electromagnetic absorption frequencies to target molecules in virions.

Absorption versus frequency graphs for various common molecules can be found at this spectral database. Also useful: Molecular Absorption Spectra.

ADD YOUR COMMENTS

Bursting the Viral Capsid

Posted February 11, 2007 by Hip
Categories: Blogroll

This is a speculative method for bursting open assembled viral capsids, even those inside a human cell, in order to destroy the virion.

It has been calculated that, for many viruses, the internal pressure inside the capsid is around 60 atmospheres. The viral DNA is squeezed in so tightly that it actually assumes a crystalline form. References: 1 2

Immediate thoughts that come to my mind are:

(a) Can we somehow further raise this internal pressure, so as to burst the capsid?
(b) And, if so, at what pressure will the capsid burst?

The answer to (b) is known: a capsid will certainly burst at when the pressure inside it is 100 atmospheres greater than that outside. This data comes from calculation on the standard method of rupturing capsids, osmotic shock. References: 1

OK, so how can we raise the pressure inside the capsid in vivo, so that it ruptures? Osmotic shock is probably out, since it is unlikely that we can radically alter salt and solute levels in the body, and even if we could, the osmotic shock generated might cause the rupture healthy cells rather than capsids.

What about heat? Can we somehow apply heat to the crystalline DNA within the capsid? If the crystalline DNA were electrically conductive, then the application of an electromagnetic field would induce eddy currents within the capsid, which would heat up the DNA, thus raising the capsid internal pressure, which at a certain point will precipitate rupture. But crystalline DNA is probably not sufficiently electrically conductive. However, it might be possible to somehow dope the crystalline DNA with some material to turn it into a semiconductor, much in the same way that silicon crystals are turned into semiconducting transistors by adding a doping chemical (usually Boron).

Assuming it is possible to make crystalline DNA semiconductive, then the application of a suitable electromagnetic field (eg: radiofrequency waves) to a virally infected patient would then heat up the (now conducting) DNA inside all the viral capsids in his body, raising the capsids’ internal pressures and rupturing them. This will effective destroy all the virions in vivo.

The problem is how to dope the DNA so as to make it electrically conductive or semiconductive. One trick might be to develop a nucleoside analog that modifies the DNA such that when the DNA assumes crystalline form (and only then), this DNA becomes semiconductive. Thus, once this nucleoside analog is given to the patient, the viral DNA (but not the nuclear DNA) in his body becomes semiconductive, and thus an externally applied electromagnetic field may be able to heat it, and so rapidly burst the virions inside his body.

Perhaps there are other ways of transferring heat to the crystalline DNA in the capsid interior? Are there any materials scientists with crystallography expertise than may offer a suggestion?

Alternatively, how about this: could a nucleoside analog be developed that operates normally during regular human cellular functioning, such as cell division and replication, but automatically disintegrates the DNA as soon as conditions of high pressure, such the 60 atmospheres found within the viral capsid, are encountered? With such pressure-sensitive DNA molecular disintegration, very few viable virions would be produced. More importantly, this type of nucleoside analog would serve as a universal antiviral, working for any DNA virus that has these high pressures inside their capsids.

These ideas are offered to stimulate the imagination. I hope they inspire further lateral thinking, so that you may come up with some more creative, practicable methods on eliminating viruses from the body.

ADD YOUR COMMENTS


Follow

Get every new post delivered to your Inbox.